Paint scratch on side
 

Should I use paint to cover this or rubberized rust proof spray? I am not really bothered by how it looks just concerned a little bit about that allowing it to rust.

I'd suggest you hit it with some touch up paint.

Prep it good first with some alcohol. NO, not YOU, the scratch - ;)

I recently touched up this area after scraping on a curb. I used primer, then truck bed liner and then dabbed it with a paint roller when still wet to get the texture right. Then I sprayed over it with a very similar paint color. I was pretty happy with the result.