The dislike for Bootstrap isn't a hate for the framework and its components. It's the fact that most people do not customize it, and so nearly all Bootstrap sites _look_ like Bootstrap. Cartoonish and bulky rounded buttons, overly large menus, etc. The default theme feels equivalent to using Comic Sans MS. It's too Web 2.0 and not very professional looking.

Properly theming (at least in 3.x) took a lot of effort. Just try to make a theme whereby at first glance, you can't tell that Bootstrap was used. It's not that it's not possible to do, it just took a lot of time and effort to nitpick over every detail.

In professional environments (ie: real flesh and blood companies), developers cannot say "we're using Bootstrap's default theme". The business has designers, the designers come up with a design, and unless the developer can customize Bootstrap to accommodate the requirements, in a reasonable amount of time to meet deadlines, Bootstrap is simply not an option outside of using the grid system.