It is cool because...
a) It could come off at high speeds
b) Even if it doesn't come off, it could slide around on the roof and scratch the paint
c) ???
d) None of the above
If the finish is compromised, over time it could cause the roof to rust. No, its probably not a huge deal and you are not in any danger of the roof collapsing, but if it was me, I wouldn't do it.
I looked at the calendar. Its December 23, not April 1. A paper towel? Is this a good idea?? Seriously??? You're kidding, right?
What I have done is to use the plastic lid of a coffee can, but you have to cut out the little thingie in the middle of the lid so the antenna sits flat agains the plastic. I used it on smaller antennas with no real problems. In your case, you are already dealing with a magnet that is barely strong enough to hold the antenna to a metal roof as it is and the plastic could cause it to slide around but probably cause less damage to the roof.
If you stick with the mag mount, you should still take it off periodically and clean off the roof. I think you really will be surprised to see what it does to the finish. Of course, YMMV!
When I meant I would leave it on permanently, I would still be removing it every week and clean the surface underneath...if I do that, will it be okay to use as my main antenna?