Does paint have transparency support? Last I recall, it didn't, and that's pretty bad if you're making pixel art for something other than just display.
I would recommend GIMP, but the people here seem to treat GIMP like a spawn of satan and Paint.NET a godsend.
imo gimp is just overkill for pixel art. not that it can't be used for it; just that for those who have little-to-no experience working with art programs, paint.net is a lot easier to grasp and has enough functionality to do most things those with little experience need.