According to microbiologist Phillip M. Tierno, aka Dr. Germ, toilet seats are designed to repel bacteria -- something toilet paper doesn't do.
Consider this: Every time you flush, bacteria makes its way into the air, landing all over the bathroom – including on the toilet paper. So if you then sit on that toilet paper you are exposing yourself to more germs than if you just sat on the seat.
According to Tierno, STDs are rarely ever found on a toilet seat and as long as you aren't exposing yourself to another person's bodily fluids, you'll be just fine.
He even says that “the top of a toilet seat is much cleaner than most people's kitchen sinks.”