Guess why they did gain popularity over time, too (Even though they were banned for use against non-heathens by the pope himself), until firearms made them obsolete.

Just like firearms, crossbows require very short training to become effective. The crossbow, however, was quickly outclassed by firearms, as the amount of power in a modest powder charge propelling a lead ball easily surpasses even the power of a very potent crossbow, which, on top of that, becomes increasingly difficult to load with increasing power. The draw weight of more powerful crossbows capable of defeating armour requires a detachable lever, or even a winch with pulleys to draw. A lot can go wrong with such complex equipment. Improperly stowing the drawing winch of a heavy crossbow between shots can easily foul the pulley system. Also, there is a significant amount of energy in a drawn (but not yet loaded) heavy crossbow. The trigger mechanism has to withstand the bow's entire draw weight, while still having a manageably light trigger pull, and you have to handle the weapon extensively between drawing an actually shooting (detach the drawing mechanism, load the bolt), which risks accidental discharge.

With a musket, you have excessively less complexity, and a safer process, because before you cock the hammer and put the priming powder into the pan, there is little chance of even a loaded musket going off accidentally. Most of the risk can be mitigated by teaching your troops the simple trick of already pointing the thing into the enemy's general direction, or at least away from themselves and their friends, when cocking and priming. And after cocking and priming, there is little handling required until you can fire.

On top of that, the ammunition for muskets is superior to that for crossbows, because it requires a significantly simpler manufacturing process. Powder can be manufactured in bulk from very few simple ingredients, and requires only the correct mixing of its ingredients. Lead balls can be easily cast by anyone who can light a fire and handle a pot, given you equip them with a suitable mould. They can also be cast in bulk. all you need is a bigger fire, a bigger pot, and more moulds.

Making crossbow bolts, on the other hand, requires quite a bit of skilled labour, and time. You need woodworking skills to make straight, uniformly shaped and sized shafts that can withstand the energy of being shot out of a powerful crossbow without breaking. The bolt heads need to be made out of iron (or steel) by a skilled blacksmith to ensure both quality and equal size. The fletching has to be uniformly cut and carefully fitted to the bolts, and so need the heads. Both have to be fitted in a durable manner that not only survives prolonged storage, but also prevents either of them from falling off when being shot out of a high-powered crossbow. It's quite an involved process.