jujutsu rolls usually go over the shoulder, judo rolls generally go right over the centre of the spine, I've never actually seen my judo group teach shoulder rolls. I think aikido does mostly shoulder rolls.
Make sure you are getting low to the ground before you do your roll. Stop pressuring yourself to drop from standing height right into a roll, it's not even necessary to do them like that once you're good at rolling, let alone when you're still having trouble.
Get as low to the ground as you can before your roll. Try rolls out of seiza, just sit in seiza then place one of your shoulders on the ground and push off with your toes so you roll over the grounded shoulder. When you can do that and you find your hip isn't bruising up anymore and you feel no pain, do it from a squatting position. Instead of putting your shoulder on the ground, just swing one of your arms through between your legs and brushing the ground and roll over the same shoulder.
Then start walking, drop into a squat and roll just as above but all in one fluid, realistic motion. Once you can do that then you are ready to do diving rolls and all that jazz.
If you are -really- wanting to get good at rolls you can be doing good, clean dive rolls in about 2 weeks without fear of injury.
Make absolutely sure your arms aren't collapsing during the roll. You will injure your shoulder badly if you continue that habit. I speak from first hand experience.