I'm trying to think of a way of explaining how to "scrunch" up your muscles where the bar rests, but have a hard time figuring it out.
Get your grip set, then kind of scrunch up your shoulder blades with a little tension under the bar, and you'll find quite a bit of natural cushion appear. Just concentrate on exactly where the bar rests and you will find you can situate things just right to make it feel more comfortable. It may take a little wiggling around under the bar before you take it off the pins to make it feel right.
Some people have a problem with the bar no matter what, even with a towel.You could be one of those that will have nerve issues even with a pad. Hopefully not. If your gym has one of the bar pads, go ahead and use that. As you progress and get more weight on the bar, it's going to get even worse unless you simply get used to it. there's always the Manta Ray squat pad thing, but I've never tried it, or felt the need yet. Maybe when I get to the point of considerably more weight