The main issue I'm seeing with bootstrap use now is lack of customization - everyone using the default colors and styles - so that when you load one of those sites, we think, "a-ha! bootstrap". It probably takes some of the magic out of a site's novelty for developers with that reaction. I'm not sure it affects non-techie consumers -- maybe it's bad if they can't visually distinguish your site, but otherwise, I wonder if they actually notice.
I spent a bit of time customizing the Bootstrap look & feel for my own site - turning that somber black bar into a bright and sunny bar: http://www.everyday.io/ (Screenshot of logged in screen here: http://dl.dropbox.com/u/10998095/Screenshots/bootstraplogged...) I also use bootstrap for the mobile (Phonegap) version of my site, and it works surprisingly well (http://www.everyday.im/learning/switching-jquerymob-bootstra...).
Thanks, bootstrap team!