She can, but it's never been as consistent as with Superman. He got the power 3-4 years after his inception, and it became part of his iconic power set ever since. She didn't get consistent flight until post-Crisis, and before that, in her most iconic television appearances (Superfriends, and I believe the Lynda Carter show) she didn't have it.
If she doesn't fly in this, it isn't going to be a serious slight against the character as some are going to make it out to be.