My daughter has much the same reaction to Omnicef (and Augmentin and Rocefin). Just a note, if/when he gets another ear infection, ask your pediatrician if they feel that Bactrim may be indicated. It is what our ENT recommends and did a great job without the side effects--and it doesn't have to be refrigerated!
My daughter is just about to get her second set of tubes...and I've tried every possible treatment (natural, chemical, voodoo, or otherwise) to get rid of the ear infections...to no avail.
If you are exclusively breastfeeding, that is the best thing to do. If you have added solids, BRAT (bananas, rice, applesauce, toast) will help slow things down. Add plain yogurt with live cultures to help repopulate his bowel--sugar and high fructose corn syrup can make diarrhea worse.
I hate to tell you, but I've had it take more than two weeks for my daughter's system to get back on track...and the kid eats yogurt everyday and will let me break an acidophilus capsule in her mouth to wash down with juice! I also brew her herbal peppermint tea and she's loved that since she was little.
If it goes on for many more days, the pediatrician will likely culture a stool sample...but they're going to want you to battle it every other way possible.