At this point in its adoption curve, using Bootstrap is amateur. It says I have no idea how to style a webpage. Yes, it makes things look "attractive", but because it so popular, using Bootstrap on a website creates a site with no identity because it looks identical to the 100,000 other sites that use it.
Aside from creating designs with no soul, Bootstrap enforces a model where people without design expertise are supposed to be somehow be good enough at design to utilize these UI components effectively.
If you are not good enough to design a website, what makes you good enough to understand the appropriate time to use a component or when not to?
Hacker News itself has a very hand rolled UI and it works great. If it got Bootstrapped it would be a drastic step backwards. It just isn't the right solution for a lot of sites. It's design overkill.
Again, I think Bootstrap is cool, but I would never use it. I don't consider myself a designer, but I'm not okay with working on things that look like everyone else. Simple + handrolled > Bootstrap.