Google Wallet's major overhaul created a kind of a workaround that allowed any credit card to work within the app. However, according to All Things D, Google didn't get an official sign off from American Express for the "additional use." The update to Wallet works by taking the functionality that already existed in Google Wallet's online product, where any credit card can be added, and then utilizing a "virtual" MasterCard at the point of sale. The result is that your own credit card is charged, but the merchant sees Google's virtual MasterCard at the point=of-sale and the charge appears on your statement as a generic "Google Wallet" line item.
That workaround solution might be the crux of the problem. The same spokesperson, Bradley Minor, told TechCrunch that “We want to make sure Google’s mobile wallet product meets the standards we set for our Cardmembers in terms of transparency and clarity about transaction detail."
Interestingly, Minor also noted that the company could "shut off" the integration. Whether it will do so remains to be seen, but we do know that the issue of fragmentation in the mobile payments space isn't going away anytime soon, Google's attempt at creating something more universal notwithstanding.