The rock would have to work it's way through the tire's fabric caseing. That's harder to do than just embedding itself in the tread rubber. It can eventually happen however and, when it does, you'll definitely get a puncture.

Bicycle tire manufacturers usually offer models with varying degrees of puncture resistance. Essentially these consist of some kind of reinforced caseing so rocks can't penetrate it as easily. The most puncture resistant tires tend to be quite stiff so they ride and perform less well. The fastest performing tires tend to be very supple, puncture more easily and tend to not last as long.