Yes, many ski hip protectors work great worn over a thin base layer and under your ski pants. This mid-layer setup is actually a popular choice for a few reasons. Your base layer can wick sweat away from your skin, keeping you drier and more comfortable throughout the day. The protector still stays in position well since it's sandwiched between your base layer and ski pants.
This layering approach is especially handy for temperature regulation. On colder days, you get the moisture-wicking benefit of the base layer against your skin, with the protector providing an extra bit of warmth over your hips. Just make sure your ski pants have enough room to comfortably fit both the base layer and the protector underneath without feeling too tight or restricting movement.