From Cory Silverberg,
Your Guide to Sexuality.
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Although the common cold and flu can be transmitted during sex, we do not think of them as sexually transmitted diseases (STDs), because it is not the sexual contact that causes the transmission, it’s just being close to the other person.

Most STDs cause problems in the genitalia, anus, or mouth (although Hepatitis B is considered an STD and infects the liver).

There are other things that seem to be related to penetration, like yeast and bladder infections, but these are not usually passed from one person to another.

Infections are caused by germs. Some germs are bacteria, which are fairly large and can be killed by antibiotics. Some germs are viruses, which are much smaller and harder to kill, although there are some drugs now that work against certain viruses. Many people who have STI germs in their bodies have no sign of this – no discharge from their penis or vagina, no funny sores. Condoms stop many viruses and bacteria, but if the germ is in an area that is not protected by the condom, then you can still get the infection.