Great comments so far...
Does the bar hurt your traps or is it on the bone of your spine?
Better shoulder flexibility should help bar comfort as you can really get the bar on muscle from shoulder to shoulder and eventually support a lot of weight comfortably.
That said, front squats are a good variant. However, I personally find them harder to get comfortable once the weight gets up there.... there's always the trap bar squat/dead lift!
"You must have a very strong reason for doing an exercise. If you don't, scrap it and move on." -Jim Wendler