Bondo!!
I had the same problem when I took my trim off. Easy fix, sand down to bare metal, bondo, etching primer, and then either paint or bed liner. I first used bed liner, than when I repainted I decided to ditch the bed liner (btw that stuff doesnt come off easily, wire brush for about 2 hours). So after the new paintjob, I ran it through the carwash, and one of those holes got knocked through, so I decided to use Herculiner this time, and not have to worry about it. So far so good
Bed liner will hold up better than paint longterm, but if you don't like the idea of bedliner, just paint it.