Quistis cared about Squall for a long time. She even thought she might be in love with him. That's a pretty big deal. She was understandably upset when an anonymous flirty stranger - Rinoa - simply came along and stole his heart almost as soon as Squall met her. She says, at one point, that she 'almost gave up' on her feelings for him. Losing any hope of a deeper relationship with Squall probably affected her quite profoundly.
Squall, of course, was either too ignorant or too uncaring to show her any kind of sympathy, compassion or friendship; but he still expected to get that reaction from everyone else each time he got upset about Rinoa.

This is shown at its finest if you choose to send Rinoa and Zell to the Missile Base with Selphie. Back at the Garden, (SPOILER)Squall tries to go crying to Quistis. She tells him to 'go talk to a wall'.Quite good payback, in my opinion. I love that scene.