That's because "everyone" uses the same basic Bootstrap themes. If you use Bootstrap for layout and responsive UI you'll be fine, it is just when you are the nth site to use the default theme with the same damn default navigation that it gets a little cringe.

So in my opinion you're asking the wrong question, the right question is: "How do I make my Bootstrap site not FEEL like every single other Bootstrap site on the internet?"

If you're willing to pay for high quality third party themes it is definitely possible to get something that nobody would call a Bootstrap powered site unless they happened to look at the raw code.

Just don't throw the baby out with the bathwater when all you really want is to look fresh, original, and on-point. It can be done with Bootstrap.