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There's this creature that swims over the surface of water and it's giant, almost the size of a whale and has thick scales as armor over its back. This creature almost never dives underwater so from afar it looks like a boat.
Why would an animal only swim over the surface of the water like a boat and avoid going underwater as much as possible?
That's where its food source is.
Most algae is found near the surface of the ocean, so if this creature has a semi long neck, it can swim gently along moving its head back and forth, up and down taking in the algae and anything else it finds.
It stays at or near the surface as it's an air breather, so swimming under the water and then surfacing takes energy. This energy is much better spent floating on the surface, occasionally swimming, and mostly moving its neck to slurp up food.
Needs sunlight
It could have a usage for sunlight. Maybe a system similar to how plants use sunlight in photosynthesis. Heck, it could be exactly that. Make it have cells with photosynthetic properties on its "back". That way, if it dives, it makes less food. It means that it can dive if you ever need that (for design reasons like mating; or for whatever story-line reason that might come), but overall it would be preferable for the creature to stay afloat.
Symbiotic relationship
Have another species live on your creature. Those are not sea-beings, and thus need air to breathe. Now you just need to find a mutual benefit in this relationship, which isn't hard (mainly because there are so many real examples to take inspiration from). Hypos for example have small animals pick traces of dirt from them. The small animals eat what they pick away. Hypos get free cleaning, small-ones get a tasty treat. This is a common thing with large not-so-mobile animals (elephants, sharks etc.).
It needs air to breathe
Quite a few sea-dwelling creatures need to raise above the sea and reach air to breathe. Usually they then return underwater, but maybe a creature the size you describe just conserves energy, and prefers to stay at air-level constantly. Moving up-and-down a large mass is a big waste of resources. Also, it might not bear the ability to "hold its breath" for long.
Buoyancy is a big deal for sea creatures. Pretty much everything living on or in water have a density that makes them naturally comfortable (i.e. energy efficient) only at certain depths, and changing depths without also changing their density (i.e. via lungs or air sacs) requires significant effort.
Take ducks, for example. They're very buoyant; they can dive, but it takes significant energy to do so. Since that's also how they get their food, they naturally evolved to be very efficient divers, but since they're air-breathers they also naturally evolved to spend most of their time on the surface.
Swans and geese, on the other hand, are also very buoyant but they don't dive. They eat mostly floating plant matter or seaweed they can reach just by stretching their long necks underwater while staying afloat.
Just floating at your preferred depth (i.e. the top of the ocean) is the most energy efficient way of living, and for an air-breather anything that involves you staying where there's air is vastly preferable to the alternative. Natural selection wouldn't really promote any sort of diving instinct which goes against both of those without a compelling reason to do so (i.e. food or survival). If your large whaleboat is naturally buoyant and able to get food without diving (i.e. feeding on surface organisms, or using long appendages to grab food from depth), and is big and strong enough that it doesn't need to hide from predators, it seems likely that it just wouldn't evolve any sort of diving instinct at all.
Hmm. A boat would have a curved upwards shape. As for avoiding depth . . .
And the most obvious one of all: Hunting. If there's a seafaring people, they'll jump for the chance to commandeer an abandoned boat. They climb in, the animal dives, surfaces again, and eats. This could also catch birds looking for a rest. If the scales are shiny, they might also mimic gold or jewels: another incentive for something (sentient) to climb on.
Terrestrial => Marine evolution
To justify such a lack of deep water related adaptations, I guess the most logical explanation would be that this creature was terrestrial in the past, and was pushed towards the marine environment by biotic (or abiotic) factors such as competition or predation. Instead of developping diving adaptations, it developped buoyancy (which could be just as adaptative!)
That also implies all of the feeding has to occur on the surface of the water. It could be:
I guess the Autotrophy part would be almost mandatory, as a mean of protection against intense UV radiation.
Other necessary adaptations would include the ability to process salt water. Exemple: using salt and Silica from sea water to create its scales (in a similar fashion to marine Diatoms)
As others have pointed out, a creature would not dive if it was unable to do so due to being too buoyant, and if it had no reason to.
As for reasons for diving, one is to get food and another is to avoid attack from aerial predators. The latter reason is taken care of by the armour, but we have to ask why a surface-dwelling organism would evolve armour instead of evolving the ability to dive, which is probably the easier solution for most organisms.
This is where buoyancy comes in. If the animal is very lightweight it will be hard for it to evolve diving behaviour, and it might take the armour strategy instead. Buoyancy means low density, i.e. light weight for the size. But why would an animal be so light weight? One obvious reason is flight.
So: we have to imagine that this organism's ancestors were birds, or pterodactyls or similar flying creatures. Think of something like a large sea bird, though not necessarily a whale-sized one. It eats something that lives near the surface, so it doesn't need to dive very deep (if at all), and it spends a lot of its time resting on the water surface, using its feet to paddle like a duck or a swan.
If food is very plentiful and predators are few, then birds will often lose the ability to fly. We just have to imagine that this happens here, resulting in a bird-like animal that spends all of its time paddling in the water, never taking to the air.
(One difficulty is that a bird would need to lay its eggs on dry ground, but if this is not an Earth species we can imagine that it has live young instead. Or it could evolve a special body cavity in which to incubate its eggs or something - you'll have to be inventive here.)
After that, we just need it to evolve its large size and armoured back. Sea animals seem to evolve a large size quite often. The reasons for this are not completely understood (though see here), but the same thing might well happen to a flightless sea bird. It would be easier for it to stay warm, it would have bigger fat reserves, and it would be so big that no predator could eat it. However, since it's sitting helpless in the water it could still be attacked by other aerial predators, who peck at its flesh without killing it. An armoured skin would be a sensible evolutionary response to this.
Maybe these are intelligent creatures with a society deep below the surface. The creature remains on the surface in order to receive something for performing the boat function as a service for another creature. It is intelligent enough to perform this action on purpose as a sort of employment for which it is given some sort of payment. Maybe the payment is something which can only be procured on land and is needed deep below the surface. Maybe instead of needing it the creatures just want this thing. Maybe they are collectors of rare dry land objects and this is the only way they can obtain these things.
Why would an animal only swim over the surface of the water like a boat and avoid going underwater as much as possible?
Because it is unable to do so.
The density of this animal's body is so much less than water that whatever it does, it is unable to go deep inside water - the same reason why a boat remains at the surface.
This creature may be a giant, primitive fish that breathes air. Its lungs, due to lacking the adaptations of tetrapods, would likely only be adapted to provide the oxygen that the fish needs, and so the fish cannot hold its breathe and dive underwater
Because it's been bred to serve as a biological boat. It has a mouth like a manta ray, which allows it to eat and breathe as it moves. Six or eight oar-like flippers and a powerful tail with two flukes at the end provide superior maneuverability. Its armored back has a semi-flat, concave surface where the people go. Steering is possible because of a flexible protrusion on the top.
This creature evolved as an extremely buoyant filter-feeding fish, the armor is to protect it from aerial predators and the protrusion allows it to sense wind speed and direction-when the wind bends the protrusion one way, that's where it's surface-dwelling food is going, so it goes in that direction. This allows for easy steering, and when the humans discovered this, they soon began breeding this species to serve as boats so they could reserve wood for other things (like construction).
