The problem with prestige classes, and the reason it isn't something that those of us who don't want to use can just ignore, is thus:
1) Prestige classes lock features into a new category. A feature placed into a prestige class is a feature unavailable to those who aren't using them.
2) Prestige classes lock concepts in a new category. Let's say some of us are looking forward to a sha'ir subclass. Except, they decide to make sha'ir a prestige class instead. Now we either have to use prestige class or miss out on the official sha'ir option.
3) Prestige classes confuse categories. Take the sha'ir example. Who knows where it will come out if prestige classes are in the game? And we get the joy of having to be concerned about where new stuff comes out for every subclass we may want (and this applies to people who like prestige classes too!) Can you imagine the tweets to Mike and Jeremy? "I'm looking forward to sha'ir, but PLEASE don't make it a prestige class!" or "I really want sha'ir to be a prestige class so my cleric can take it!" There isn't much argument about whether something should be a feat or a subclass--they are generally pretty obvious. Prestige class vs. subclass is a can of slime covered fiendish rune-worms waiting to happen.
Because of this, prestige classes alter the game for everyone, even those of use who choose not to use them in our games. Unlike multiclassing, they affect all of us, because they change the way future design happens. I don't like prestige classes, but more important than that, I don't like the way they change everyone's game, regardless of whether they choose to use them.