For a serious answer, yes. If squatting with the bar is uncomfortable, you need to build up your muscle shelf in your back. You also may have the bar too high and if you don't have big traps, it'll be sitting on the top of your shoulder bones and that hurts. Also, making sure you pinch your shoulder blades together and keeping the elbows tight helps to bunch the muscle together.
The pad might also throw off your groove a little on bigger weights because the bar and weight won't be quite in the same spot as it would resting directly against your skin.
Same with anything else in lifting - it'll probably hurt the first couple of times and then your body will adapt.