Please consider that: 1. Almost no one in the world has heard of Bootstrap. Though it's captured our mindshare as developers, most of our users will not know nor care if the app is Bootstrap or not. 2. The vast majority of web apps still will not be Bootstrap apps.
Basically none of the general public will say "Hey, this is a Bootstrap'ed application, I'm not using it." They just do not know nor care what Bootstrap is. If it looks professional and works as they expect, they will be happy. If they're happy, I'm happy.