The Bevelle thing is a bit... odd. From searching around, it seems that Sin has taken a shot at Luca a few times, but the Crusaders work hard to rebuild it quickly and do everything they can to protect it.

As for Bevelle, there are a few theories. One is that most of Bevelle's machina is underground and/or well hidden as illustrated by Wakka's shock at the large amount of Machina he sees at Yuna's wedding. I am not a fan of that theory. The second one is that Sin mostly attacks coastal towns (Kilika) and things out in the ocean (S.S. Liki, the Al Bhed Ship) because Dream Zanarkand is located out in the ocean near Baaj Temple and part of what Sin does is protect Dream Zanarkand. That's also one of the reasons Yu Yevon wanted to stunt technological advancement is so no one would discover Dream Zanarkand. Bevelle is very much inland, and thus less of a threat. Or you could blame it on bad writing if you want to. It is after all a work of fiction meaning it is possible some stuff just doesn't have an answer.

If it is the second one, you may wonder how no one had discovered Dream Zanarkand. The answer to that seems to be that any ship that goes near it will be destroyed by Sin, and when Cid gets the Airship, its basically a first and they hadn't had time to go exploring and find it, especially since they weren't totally clear on what to look for and where to look for it. Plus they were preoccupied with the whole deafeat Sin thing.

Something I've never understood is why Sin attacks Dream Zanarkand in the beginning of the game. I assume it was to bring Tidus to Spira, but it is never totally clear. Maybe because its a dream, Yu Yevon can basically continue Dream Zanarkand as if Sin had never attacked it, minus Tidus who is now gone.