the sex may simply be vigorous and his penis is a bit sore afterwards. this is fairly common if you have several sex sessions in a day.
some men (and indeed women) can have an allergy to latex. if you are using condoms this could be the reason why. it is possible to buy non-latex condoms as an alternative.
perhaps you are not wet enough when you two have sex. you could try buying some lubricant to ease the friction a bit.
it is probably unlikely that he has an infection of any kind, because the pain would surely manifest itself at other times, not just straight after sex. but nonetheless if you try all these things and it still happens, he could get it checked out.