It's pretty common, actually, especially with the barefoot shoes trending. It's not the best thing to do if you're a competitive weight lifter, as you would then want the weightlifting shoes with the heel lift in order to receive extra stability. But if you're using the barbell for fitness, then going barefoot will actually be better, as you're stabilizer muscles will have to fire. It may also help lengthen your calf muscles since you're heel will be in contact with the floor.
Keep in mind that not everyone is able to do barefoot squats, though. If you don't have the calf flexibility already to do a squat without your heels lifting off the ground when you're barefoot, then take some precautions and ease yourself in being able to maintain that contact.