There will always be more Mages in a raid than Hunters, unless they can't get any Mages because there aren't any available.
Hunter is definitely more engaging to play. More complex rotation, pet management etc. That being said, as a Hunter you will always do less DPS than an evenly geared and skilled Mage past BWL. In MC and BWL it's about the same. Mage is much, much easier to play, especially on Alliance side because you get Blessings to give you mana and reduce your threat (which are the two biggest difficulties to manage when raiding as a Mage). Don't expect to be top DPS in a guild with competent players, and you won't be disappointed. As a good Hunter you'll get recognition anyway, because good Hunters are rare and bring nice boons to the raid.
Hunters have a pretty high skillcap, even in PvE. There are so many things you can do to improve the speed of a dungeon run for example. Toggling Aspect of the Pack to travel faster, putting a Freezing Trap under the healer just before the pull. Looking out for the healer if he pulls aggro. You wear mail and can kite, if the healer pulls aggro, Distracting shot the mob and kite it, or have your pet Growl/Intimidation and tank it. Chaining Freezing Traps with Feign Death and some kiting. Frost Traps so Mages can focus on Arcane Explosion instead of Blizzard (AE does WAY more DPS). Those are just some of the things that make good Hunters stand out from the masses.
Mages are more wanted overall because they are the better class, objectively. And it doesn't help that Mages scale better the more you have of them (due to Winter's Chill and Ignite). But that doesn't mean Hunters are bad. Hunters still bring good utility to raids (Tranq shot, Trueshot Aura) and can still push out good DPS. You'll be on par with Mages and Warlocks in MC/BWL. It's in AQ40 when those casters get sick gear that Hunters really fall behind.