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Diaper rash is the worst!!! Here's what I wrote up on my blog about it (link here: http://tinalimchung.xanga.com/742938397/good-day-bad-day/)

Diaper Rash is normal and happens to all babies. But it is a horrible thing. Peeing and pooping is very painful for baby, and changing the diaper makes them scream. I've read so much about it and talked to our pediatrician about it, because the last time it happened it was really really bad. It was so bad and hard to get rid of that I have since been extremely vigilant about keeping RJ's bottom dry and rash-free. So I was shocked when this case came out of NOWHERE. And it's just as bad as the last case. I was a little in denial about it until today (he doesn't even have diarrhea! why does he have a rash???), but it wasn't getting any better so I've finally switched into crisis mode. Here is what I've learned about diaper rash.

How to prevent diaper rash
The general idea is to keep baby's bottom clean and dry, and use diaper cream to prevent friction on the skin.

Change diapers OFTEN. Don't let baby stay in a soiled diaper, ever. This is especially important when baby is having soft poops. Change poopy diapers immediately.
After wiping, let baby's bottom dry COMPLETELY before applying diaper cream.
Always apply a thick layer of diaper cream all over the buttocks, deep into the crack, and in the creases where torso meets legs. Honestly, it doesn't matter what diaper cream you use-- people swear by Triple Paste or Butt Paste but I find the Desitin I buy at Costco works just as well, if not better.
At night, when you know baby will probably have to sit in a soiled diaper for hours, complete all the steps above but apply SEVERAL layers of diaper cream. The idea is that when you get baby in the morning, there is still at least a thin layer of cream on the skin.

How to treat diaper rash
As soon as you see any sign of rash, start employing the technique below immediately until the skin is completely healed and back to normal. It takes a lot of effort during every diaper change, so plan to stay at home a lot and assemble your materials in a central diaper changing station.

Fold a small towel in half and lay on the bottom half of the changing pad. Lay baby on top and unfasten diaper. Fill a bulb syringe (the thing used to suck snot out of a newborn's nose) with warm water and wash baby's bottom, letting the water drip into the diaper. Use diaper or wet washcloth to clean off poop. Take the diaper out and use the towel to pat the skin dry.
Let baby hang out without a diaper or bottom for at least 10 minutes to make sure the skin is completely dry. I pull up the front and back of his onesie over one shoulder and snap it in place and let him walk around and play or watch TV.
Once skin is BONE dry, position diaper under baby and apply a thin layer of Clotrimazole (over the counter cream, better known as Lotrimin, yes, athlete's foot cream). In case yeast is involved, this ointment will kill it.
Now apply a thick layer of your favorite diaper rash cream. I use Desitin creamy because 1) I can buy it in 2 packs at Costco, 2) it comes in a tube, making it slightly less messy to use, and 3) it seems to work just as well or better than anything else I've tried.
Once you've added a thick layer all over the buttocks, deep into the crack, and in the creases between torso and legs, add another layer. (If you think you have enough, go ahead and add another layer. The idea is to have plenty of cream so the skin never rubs against the actual diaper.) I usually have lots of cream left over on my fingers, so I smear it onto the diaper in the area where the butt will hit.
Put on diaper!

At the hospital I work at, we have had good luck with using a 1:1 mixture of lanolin and silicone barrier cream on sore bums, we also let the bum dry out by leaving the baby diaper-less, cream less and wrapped loosely in a bunch of blankets while they sleep (to avoid pee/poo staying in contact with the rash - of course then they need to be bathed after).

And keep going with the diaper-free time as much as possible.

Agree with everything PPs have mentioned so far. Just wanted to chime in and ask if there's fruit in the yogurt that you're giving him? I've noticed that fruits and juices tend to be a culprit of diarrhea that begets diaper rash. That could exacerbate the loose stools that the meds are already giving him. If there are no fruits/juices, just ignore me
Good luck!

Like @Livsmama said, it could be a yeast infection since it's antibiotic related. Yeast diaper rash looks different than regular diaper rash (see a picture and description here: http://www.babycenter.com/0_yeast-diaper-rash_10913.bc). If that's the case, you'll want to use an anti fungal cream rather than a regular diaper rash cream. We've used monistat at the direction of our pediatrician, and it worked for us.

I'm no expert, but my sister always had a blow dryer on hand, so her LO after being changed and wipe had a very dry bum before she put on any ointment and the diaper.