In the space between planets, there's really no point in flying your own ship. You're probably traveling at some hypothetical faster than light speed, and there would be nothing to do. That only leaves orbital flight, and in-atmosphere flight. If they allowed in-atmosphere flight, it would negatively impact exploration in Destiny. Say there is some weapon hidden on the top of some mountain, and you have to trek up some overgrown trail to reach the summit. That could all be skipped if you can just fly up to the top. So the only place left to allow flight is in orbit around planets or other objects. But think about how sterile an environment that is. Sure the background will change, depending on where you are, but space is otherwise empty. There are no paths to follow, doors to unlock, treasures to find. The only activity of any real entertainment value would be dog fights. Now sure, a dog fight would be fun once or twice, but I don't think it's something people would end up going back to much. Not when there's a planet below you with loot to find.