A.L.
Most Rash Guards are 50 SPF. A plain t-shsirt is probably more like 5-10 meaning the sun can penetrate the material. Rash guards are made to dry quick so you're not left with that saggy wet feeling of regular clothes.
I'd keep making him wear the rash guard, and get it with long sleeves so you don't have to apply sunscreen except to his face, neck and legs. That's what I do with both of my kids because they HATE having to put on sunscreen every 30-45 minutes...If there's less body area to apply it to, the better. :)
Good luck!