I'm looking for plausible reasons or obstacles that would help explain why traditional jet/rocket/prop-based air travel is not practical
Well, not exactly your ordinary columba livia domestica, but pigeon-analogues nonetheless. They live almost everywhere, breed like crazy, and luckily, unlike their Earth cousins, dislike the noise and smells of human cities and keep to the brush, fields, and undergrowth.
They're mostly harmless, except that they have this reflex - perhaps evolved to deal with very large predators, now understandably extinct - to swarm and attack whatever flies and is sufficiently larger than them.
They will roost on an airship and tear it to pieces in a killing frenzy, they'll overload the most powerful armored drone, and they will kill themselves smashing against a landing shuttle at the highest speed they can attain. And they will foul all kinds of enclosed or non-enclosed propeller with their pseudo-feathers and down and blood, choke jet engines with their bodies, and nine times out of ten they'll even succeed in killing anyone that succeeded in ejecting unless they reach the ground quickly enough to make the attack stop.
In the country, boys will dare one another to fly kites, to watch clouds of shrieking berserkers tear them to pieces.
Poisoning the pseudo-pigeons is impossible without covering the planet with poison; gengineered pathogens risk destabilizing the whole ecosystem; introducing predators is hopeless because they'd be swarmed under; the best that can be done is flying at night, losing one plane in ten, which is totally unaffordable, or using armored, slow airships, which are even more uneconomical; or using orbital shuttles that take off at high acceleration using ground-based lasers, and perform combat-drop landings; which is the most expensive option of them all, even if it is done to land tech, outworld supplies, and personnel since it is, after all, the only way.
Once an experimental project aiming to teach them not to chase fliers, using hundreds of large rocket-propelled cut-out shapes, floundered against the hard fact that the alien pigeons were just too stupid to learn, and attacked the thousandth fake plane with the same reckless abandon of the first, Earthmen decided to leave the alien skies alone.
So, railway it is.
Can't live with them, can't profit without them
Albeit dubbed pigeons because of size and general shape, our critters aren't really pigeons; to be sure, they're not Terran birds either. They don't behave like ones, nor do they reproduce the same way. The passenger pigeon was adapted to its environment, but vulnerable to anthropization. The main vulnerability was the existence of nesting colonies. Disrupt the colony, extinguish the species. Our critters are solitary and r-strategists, more like insects than birds, and have managed to monopolize the air; the ecosystem has adapted so that they are the only long-range pollinator species, the main source of protein-analogues for a host of scavenging organisms that also improve the soil (okay, worms), and several arboreal species have co-evolved so that their seeds are now only viable after passing from a pseudo-pigeon's digestive tract (presumably quite far from the parent organism). In short, not only would removing the crazy psycho-pigeons be exceedingly difficult, it will involve a long-term ecological nightmare.
Which we can't afford because it turns out that the precious compound found in the soil is in all likelihood a breakdown product of some kind of complex polyterpene associated with some of those plants' pseudo-bark. The exact chemical makeup and synthesizing pathway not having been successfully investigated yet, much less reproduced artificially (and nothing guarantees it won't be horribly expensive anyway), the various interests on the planet simply do not dare meddling too much with the ecosystem.
What they can do (and do) is harvest reasonable quantities of pseudo-bark from promising copses, and send them by rail to the processing plants.
Railways are deployed by track-laying robots and are reusable, light and sturdy enough to go practically everywhere. It would be possible to prepare covered, protected airstrips where a computer-controlled plane would enter at high speed and leave at high speed, but it would cost much more and not be as flexible as rails. The impossibility of long-range communications with planes (and of using radars) also reduces their appeal. What would really be useful is helicopters, but those are out of the question: they'd need to fly slowly and from, or to, pigeon-rich woods, exactly the thing one shouldn't do.