Allergy to latex is one possibility as is prostatitis (inflamation of prostate) which can be caused by overuse or unusual frequency. If you are allergic to latex, you should likely see some skin irritation. If the discomfort feels deep, it's more likely your prostate. Try a hot bath a couple of times a day and refrain for a couple of days if it's prostate. If you develop a fever or strong pain see a doc as you might have a prostate. infection in that case (not STD).
Its possible if your using a latex condom, you might be illergic to it. Im not a professional and im a girl, but i know if i use a latex condom anytime i burn and itch and have irritation after i pee too. I found this out when i was 15 that i couldnt use latex. they have other materials at the drug store, sheepskin for example. However if you have been using a condom for years and never had any problems im not sure what the problem would be. try switching to a non latex condom for a while andsee if it helps. if it dont and its really bothersome, go to the doc.