I love squatting on Smith machines. Dorian Yates used Smith squats exclusively during his Mr. Olympia years, because it isolates the quads and hamstrings really well without all the balance issues involved in free squatting. Like anything else it takes some getting used to. You need to experiment with different feet and bar positions to find your comfort range, since everyone is different. I find I like to have the bar higher up on my shoulders than when free squatting. Squat with just the bar next time and try different things.