Technically, at least against pregnancy, sex while on oral contraceptives is protected sex. As mentioned before, it's still best to use a condom. Not only to protect against std's, but why only use one method when you can use two and have that much less of a chance of getting pregnant?
Taking plan b, from what you'e told us was unnecessary and the most likely reason your cycle is now off. I agree with orphan again, seeing you dr to make sure (and why not get tested for stds while you're there anyways) is the best advice.