All windows apps look the same. And all Mac Apps. Maybe Bootstrap is the beginning of making all things web look/work/feel similar to on another. Is that terrible?
I'd dispute that any of my apps on OS X or Windows look the same, except those from related product families like Office. Safari doesn't look like Chrome. Mac Mail looks nothing like iPhoto, etc...
In addition, skinning desktop software is generally seen as bad practice and apps that do it stick out like a sore thumb.
No! It's not terrible at all. Not to me anyway. I'm always pleased to find another bootstrap app because I already know the UI conventions that it'll be using and it looks great.
If you work as a web designer (technician, really) it might be.