I'm sure the idea here is "oh, I'm just making a quick MVP, or even a pre-MVP, or a weekend project, and Bootstrap makes the design super easy!" But if you're not going to change it at all, you might as well stick with browser defaults and not include a stylesheet at all - at this point, uncustomized Boostrap looks just as tacky as a site that was black serif text on a white background with blue and purple links.
It's easy to fix, and it's fun. Just take an hour to experiment - your site deserves it. Change up the fonts! Get a nice header font, especially if you're using a big "Hero" badge. Look at the Google Web Font gallery for some inspiration. Get some unique colors - different shades for different elements, build a nice visual hierarchy.
Drop the top nav bar, unless you're doing docs or something that could actually use it. It looks a bit tacky, especially "position: fixed", when it's unnecessary.
Now, on the other hand, you don't have to change everything. Leave the button gradients as they are, the grid system isn't exactly going to stick out, etc. You just need the overall look of your site to be unique - individual elements don't matter as much. http://www.savng.com/ is built with Bootstrap, but you couldn't tell it unless you really were looking (and thus noticed the "Add a deal" button and the pill navs at the bottom).
Just be a bit different. It's easy, and rewarding.