I think this prejudice only exists within this community where if you aren't that special snowflake you're not cool. I'd guess 99% of web traffic has no clue what Bootstrap is, what it looks like by default, how it is different when it is skinned. I would guess more than anything that they just think, this is what a website looks like now-a-days.

I'm happy to use it too with very minimal tweaking because it looks good out of the box, way more pleasant than browser defaults, it works well, fairly well maintained.