Yes, they can.
Depends on how polluted the rain water ends up before it hits your paint. Some can suffer from acid rain which will etch the paint.
Even clean rain water that sits and dissolves contaminants previously on the surface can etch the paint, or leave mineral deposits.
If its dried deposits that haven't etched the surface it should come out with a cleaner wax or light polish.
Etching can be harder to remove (or not at all) depending on severity.
If you're worried about rain, take total precautions for bird droppings. :hairpull
