Your son is three? Is he potty training, yet? Getting him out of diapers and preventing feces from touching his sensitive skin might be the key.
One of my sons had this problem during his first year. He had SUCH sensitive skin that every bowel movement - no matter how quickly we got that diaper off him - would just cause his little bottom to bleed. When he loaded a diaper in the middle of the night, I'd wake up to cries of "OWIE" which absolutely broke my heart.
We used antibiotic ointment (Neosporin) on each sore and SLATHERED Desitin all over his bottom every single time we changed his diaper. The ointment was also a painkiller, and the Desitin would protect his skin from being burned by urine or more feces.
We'd also leave the diaper off of him as much as possible and let him run around naked. (I have a carpet steam cleaner and just whipped it out to clean any messes.) The exposure to air really made a difference. We also made a point of giving him bananas at every meal and making DARN sure he wasn't eating anything that could cause "hot poo." This seemed to help decrease the effect the feces had on his skin.
You mention that you work full time. Is your son in day care? Are you certain his caregiver is getting him out of dirty diapers quickly, cleaning him properly, and/or using ointment and Desitin regularly?