Cases Collect a Lot of Dust
It’s been said many times that your phone has more bacteria than a public bathroom, and that’s without a case. Imagine how dirty your iPhone can get when you keep it inside a case for a really long time.
While the iPhone is dust-resistant, that can still affect it in the long run. Likewise, it can also affect you and your respiratory system if you aren’t careful.
It’s not true of all cases, but many can collect a lot of dust if you leave them on for a very long time. If you don’t clean your iPhone regularly (which you should), then you’re just making it dirtier than it already is just by using a case.