I once got to do a tour of a historic fort, and when we visited the magazine the guide told us that garrisoned soldiers were issued wooden button fly trousers. They couldn't use a zipper because a spark might set off the gunpowder, and also they hadn't been invented yet.
I have both kinds and I don't really care. I just buy the pants because I like how they look, don't even check what kind of fly they have. I have the ones with a regular zipper and 1 button, zipper with 2 buttons, no zipper just buttons, a little hook thingy button and fly combination. There are more important aspects of pants for me, like the fit, feeling, price and how they look.
I use both, but I actually prefer the button fly. When you bust through the bathroom door and gotta take a piss, you'll appreciate being able to unbutton them all instantly with one hand as opposed to the zipper which will break or jam.
They're pretty common on raw denim, especially if it's unsanforized (i.e. not preshrunk). It's basically because when jeans stretch and shrink zippers can look weird (have you ever gotten that weird pants boner around the zipper?). They also have a fade pattern that's pretty classic. I dont think they're any less convenient than a zipper once they're broken in and you're used to them.