I am, by no means, an expert on this subject, however I would imagine that USAA has to do some administrative licensing agreement with AMEX before they can enable AMEX-branded credit cards for ApplePay.
I just called USAA to validate my MasterCard. I was transferred to a 3rd party call center that took care of the validation. I asked about getting my USAA AMEX tied to Apple Pay and was told that was expected to to live March 31, 2015. So give it a try then! Hope the person was correct.
Despite no official word on implementation, i was SUCCESSFUL today in adding my AMEX card to Apple Pay. You will have to call in at one point to an automated system, and I needed to speak with a representative, but the bottom line was it worked.