Quite the contrary. Shor's algorithm actually works better for the shorter keys of ECC. The rule of thumb is 2n qbits for RSA keys and 6n qbits for ecc. I believe it has something to do with hownit applies to the hidden subgroup problem of finite abelian groups rather than factorisation, but I am really not a cryptographer not especially mathsy. I just asked the same question you did, and someone in the know pointed me to that.