I had this problem too for a while. I get chaffed more so when I run than when I cycle. I found a seat that fit me better, and kept my legs from rubbing together so much. After that I haven't had much of a problem, and I wear boxer briefs / tighty whities with gym shorts. Admittedly, I usually ride less than 15 miles at a time, and do all my rides when its cool in the morning, but the seat seemed to help the most for me.