As a others have intimated, I think it's because they're (now) such a corporate mega-company. This isn't necessarily indicative of the quality of their bikes, but they do come off as a soulless, crassly commercial entity.

While I certainly harbor no sort of vendetta towards them, I'm much more partial to more quirky, pragmatic makers like Surly. While Surly is certainly a multi-national brand (owned by QBP), it's my understanding that they're still managed/operated by the same persons who started the company.

Again, I don't have anything against Trek; I just don't think much distinguishes them from Specialized, Diamondback, Marin, or most of the other mega manufacturers.