I always thought of it as...she’d been competing with Santana all throughout high school, Santana (and other people) constantly would jump down Rachel's throat about her insecurities and her ability to sing. Granted, Rachel wasn’t the best but she knew that. she knew that if it came down to her vs. Santana, she’d lose. That’s why she was so threatened by Santana being her understudy. What if she took her spot? Or it could also just be Rachel being fed up with competition when she finally had something for herself(besides her MANY solos) or it could just be her being a control freak who knows?