I do them as heavy as I can, they are the reason my chest blew up, and is increasing. I am a fan of the fly!
If you do them with proper form, I don't see why your shoulders should be hurting. I do them as heavy as I can and I don't have any shoulder problems.
But like Shakes said, it's all about tension (contraction). You want to keep your chest tense, or contracted, throughout the entire movement. I do like to get a good stretch at the bottom of the lift, but there's a differene between a good stretch and stretching too far. You kind of have to figure out your range, but a tad lower than 90 degrees is about right. Also, at the top of the movement, I like to squeeze my chest muscles for a brief moment, causing further contraction and muscle fiber stimulation.
Try doing a superset of incline DB flyes followed by cable crossovers, imploying the techniques described above, then after your superset, flex your chest as hard as possible for about 15-30 seconds. I love it!
The chest is a tricky muscle group to train. Some people are gifted enough to where they only need a handful of pressing movements to develop a full, powerful chest, while others, like myself, need a multitude of exercises to hit the chest from as many angles as possible. Trail and error until you find your groove, then consistency. That's my two cents anyway.