Dillon asked me a very good question: "Where did the concept of Main vs. Alts come from that you know of, and how does it stick around so well?". My first character to ever hit the level cap in any MMORPG was my warrior, but that isn't my main. The character I played the most in the last two weeks is my mage, but that isn't my main. My main is my priest, who due to Real Life® preventing me from raiding recently didn't get played much at all. So where is the logic in that?
The answer is that the concept of main vs. alts comes from raiding. Many raiding guilds, even casual ones, have rules in place that you can only raid with your main and not your alts. To understand why, you need to understand the whole concept of raid progress: Nearly all raiding guilds not only want to raid, they also want to make progress in raiding, moving from entry level raid dungeons up to more difficult raid dungeons. Not only do the higher raid dungeons give better loot, but also raiding the same place every week gets boring pretty fast. Raid progress is a guild matter, individual players can't do very much about it except giving their best. Many of the rules that raid guilds put into place are designed to promote raid progress.
If you always play the same character, and visit the same raid dungeon repeatedly, two things will happen: You learn what to do with that character in every encounter in that dungeon very well, and you'll pick up a complete or near-complete set of epic gear from that dungeon. Both the gear and the experience on how to play your class help you and your guild to advance to the next dungeon (although people have differing opinions on how much of that effect is gear and how much of it is skill). If you did the same raid dungeon the same number of times, but evenly split between two different characters, guild raid progress would suffer. Instead of having one very well equipped toon you'll have two half-equipped ones. And instead of knowing how to play one class extremely well you'll know two classes reasonably well. That has an advantage of flexibility if a raid group finds itself short of some class but in excess of others. But overall it slows down the raid progress of a guild.
Rules against alts are in place because perversely the less you contribute to the success of a raid, the better you get rewarded. If you think of a mixed group of people using their main for the umpteenths time in the same dungeon and some new players or alts, the players with more experience and better gear are obviously contributing more to the success of the raid. But as they already have most of the gear from that dungeon, they only get the badges, while the new players and alts end up with several epics. Actually TBC improved that situation a bit, because before there were no badges at all, and due to now much smaller raid groups the number of epic drops per player increased. But before TBC there were some guilds that had DKP systems that were so strict that they'd disenchant epics in spite of a new player in the raid being able to use them, just to discourage "freeloading". The source of the problem is the random loot tables. Maybe some future implementation of raids will have *only* badges and no random loot, so sticking to your main would become more of an advantage. Until then WoW is pro-alts and anti-mains, and it is up to the players and guilds to counterbalance that.