3 days late is hardly something to worry about. Every woman experiences cycle glitches now and then. And yes, a change in schedule, an increase in stress, can alter your cycle. Few women have a clockwork cycle, with a period arriving every 28 days on the dot.
After I started grad school, I didn't have a period for 3 months. I think I took half a dozen pregnancy tests, all negative. If your period doesn't show up for another week or two, you might want to take a test, but it's most likely that your cycle is just a little screwed up at the moment.
You said you had "protected" sex -- what does that mean? If you are sexually active, you should be using a really reliable form of birth control, which isn't condoms. They're good for disease prevention (though not perfect), but they are not the greatest method for pregnancy prevention. If that's all you and your partner are using, then YOU should also be using contraceptive jelly, which you can buy in a drugstore without a prescription. Use fresh jelly and a fresh condom for each act of intercourse.
But the pill, an implant, or an IUD would be a much better form of contraception.