If you want a realistic way to balance such creatures, you need look no further than thermodynamics. There are a few ways it could work out.
Fighter Plane Dragon
Say 4 tons of dragon meat wants to fly over the city and burn it to ash. Just getting him off the ground and letting him manoeuvre well enough to avoid catapult stones with powered flight is probably going to take about 1500 horsepower, and that's if he's as aerodynamic as an airplane. For reference, the "horsepower" unit gets its name by being the approximate amount of power generated by a large draft horse. Which means that this thing needs to consume as many calories as 1500 horses just to fly. Using a breath weapon requires more. Ballpark estimate: 25+ cows/10 hours powered flight.
To deal with this kind of dragon, just prevent it from eating. Use small parties of expert archers to track and harass it whenever it tries to stop and eat. Shoot a few arrows at its eyes so it has to take off to fight, and then scatter and hide. Even if it gets a couple of the archers, it won't recoup enough calories to make up for the takeoff. It will probably be too weak to be a threat within a day or two. (If it doesn't just leave the area entirely.) Alternatively, feed it a large meal, and then attack it while it's still digesting. A few extra tons of food in its gullet will make it sluggish, if it can fly at all. Throw nets and rocks at it until your town has a "dragon hill" on its outskirts. Plant some trees and a monument atop it and make it a park.
You can get around the food requirements by reducing its power output (and therefore its weight.) Make it a one-ton dragon with a power-weight ratio similar to that of large birds. It will prefer to attain takeoff velocity by leaping from high places, and its rate of ascent will be slow unless it can take advantage of thermals or other updrafts. It will probably still need at least a few hundred horsepower to move that much mass, so it's still going to be a hungry fellow, but more napkin math from the mammilian horsepower/calories numbers that I remember suggests that we'd be down to about 3 whole cows per 10 hours of flying. Give it a hummingbird like variable metabolism so it doesn't waste energy when it's not flying and a propensity to take long naps in the sun and it shouldn't be too ludicrous a thing to find on a sufficiently lush world.
This kind of dragon will likely hunt by swooping down from a high altitude and snatching some large pile of meat to carry off to a safe place to eat, similar to a hawk or eagle. Conservation of energy is a must for it since it doesn't have the sheer power necessary to just fly straight up. This kind of dragon is more likely to attack a settlement's herd animals than its buildings or people. People just aren't filling enough to be worth the effort, and attacking buildings will cost it too much velocity to regain a safe altitude unless it uses fire. To fight this kind of dragon, you just have to force it to use up its velocity. Build your towns among twisty-windy rock formations to force it to spend energy changing course. Find a spot with a down-draft or a lot of turbulence in the air and it'll just stay away entirely. Catapult-thrown nets or buckets of gravel that could damage its eyes will force it to dodge and lose speed. Trained birds could likely harass it and it would have a difficult time getting away. Just keep forcing it to dodge and eventually it will be forced to the ground. Then make the above-mentioned dragon-park. Alternatively, stretch a cow hide over a large, cow-shaped rock and watch it face-plant when it tries to grab it. Be ready with the nets and rocks. It should be relatively easy since it will require a running start to get airborne again. Just keep tripping it. Ditto if you can catch it getting a drink from the river or something. And if you can track it to its lair and sneak up on it, the odds of being able to lay some kind of trap are pretty good since it needs either a running start or something to jump off of.
This one uses lighter-than-air gas and flies like a dirigible. It will have to be relatively large for its weight and will have a lot of air resistance to overcome if it wants to fly fast, but it can cruise around like some kind of giant manta ray and devour anything that looks tasty at its leisure. It can make its home in the clouds where it can't be attacked without flight capabilities. This is probably the most dangerous of the dragon types.
It's weakness? The only floaty gas it has access to via standard metabolic methods would be hydrogen. It might be able to get a few others, but they're all corrosive, explosive, or both, and hydrogen is the only one that wouldn't cost it a huge amount of energy. Helium would require it to digest many tons of rock, and it would be dependent on deposits of minerals that are rather rare and usually deep underground.
In any case, if you can puncture the gas bladder (which will be most of the creature) it falls to the ground and you make with the nets and rocks. Assuming of course that you don't puncture said bladder with a flaming projectile and then watch the villagers rejoice as pre-cooked dragon-kibble rains down from the sky. This dragon is more dangerous until the villagers develop weapons sufficient to puncture its hide, and then it rapidly becomes the least-dangerous type and possibly a prey animal for humans.
Yes, dragons can be armoured with scales and such. But every pound of armor is a pound of dragon that's not producing thrust or lift. The numbers I've used assume that the vast majority of the dragon is flight muscle, and the most generous numbers I can find on muscle power output barely make it possible.
Scales sufficient to stop arrows when the dragon is 300 feet up probably wouldn't be an issue. Scales to stop a ballista bolt at that height? Only if you want a lumbering air-barge that's an easy target for half-ton catapult stones. Armour to stop the stones? Forget it, you're into the realm of collision physics. Even if you stop the penetration, the sheer mass of the impactor is going to swat the poor dragon out of the sky like an errant fly. Even if it survives, it still has to contend with the villagers and their nets and rocks now.
Wing membranes and joints will be rather delicate (comparatively anyway) regardless since flapping armoured wings will waste a lot of power. Let someone with a heavy crossbow or longbow get within 30 yards and they can probably hurt the thing, especially if they're a good shot. Eyes, by their nature, have to be kind of squishy. Arrows stuck in the back of the throat or the tongue could easily make it impossible to eat. Keep in mind that injuries to the wing membranes will slow the dragon down substantially and will take a very long time to heal without stitches, and if you're riding too close to the strength limit of the structures in question in order to get enough power at a low enough weight to do what you want, then a single puncture could cause catastrophic wing failure as the membrane snaps under the imbalanced strain like a bursting balloon.
People underestimate just how much energy is involved in a breath weapon. Why do you think there aren't any critters larger than insects that use such things? Assume that said breath weapon is some kind of napalm-like compound. If we use kerosene as a model, one gallon of the stuff will set the critter back about 35,000 Calories, not including any energy losses incurred in manufacturing it. Assuming perfect efficiency, every 40 gallons will cost it another cow's worth of food. That's not too shabby, but it's not something it's going to want to use willy-nilly either. It would be enough to burn down a village of straw huts, but a village of stone huts with slate roofs might take several cows worth of napalm to do any serious damage. Also, every gallon of kerosene weighs almost 7 pounds. One cow's worth of kerosene would be almost 300 pounds, which would be almost 1/6th of our creature's bodyweight (for the light version). Odds are good it doesn't carry more than that at a time, and that it takes a considerable amount of time for it to regenerate. Keep your forces spread out so it's not an efficient way of killing things until it's used up, and then proceed to the beatdown.
As an alternative, the breath weapon could be like the one used by Pernian dragons, where some local substance that they eat provides the fuel. This offsets the metabolic costs (but not the carrying weight unless it's something more energetic than hydrocarbons). But it makes refuelling on-the-go impossible. In this case, just make the substance rare enough that the dragon can't get it just anywhere, and the humans can find and booby-trap the sources. If they do it right, they should even be able to skip the dragon-beatdown part of the story. If they can't, then they weren't sufficiently creative in their use of what has to be a fairly volatile substance.
This is really the thing, isn't it? If the dragon can fly and the people can't, then a sufficiently smart dragon wins every time. It just picks up the biggest rock it can carry (probably at least a thousand pounds) flies up as high as it can (probably over a thousand feet easily) and drops its weapon from perfect safety. Repeat until the town that has annoyed it is nothing but a series of impact craters. Stay above the clouds in transit, or fly in a large loop so the silly humans can't track it back to its nest.
If it's that smart though, then there's a good chance it would realise that a symbiotic relationship with humans would be far more beneficial than an adversarial one. Humans would certainly be willing to feed such a creature in exchange for protection from other larger predators/enemy nations. And a dragon's sheer muscle power could easily help them build the infrastructure necessary to produce far more than the three cows/day it requires, (assuming it's not content to just hibernate whenever it's not needed, in which case it'll need far less overall.) The best defence against wild dragons is domesticated ones. (Cue storyline about the hero saving the heroine from being sacrificed only to discover that killing the dragon means the truly big predators can move back in now...)