As Clark Lindsey (and Keith Cowing) notes, NASA hasn't formally dropped methane propulsion from Constellation, or CEV. The final CFI doesn't, after all, forbid methane, or specify hypergolics. They simply appear to have dropped it in the final version because the earlier draft version of the CFI so emphatically required it.

However, given the risk aversion of industry, it's almost a foregone conclusion that neither bidder on CEV will propose methane propulsion, absent a strong sense of a desire to have it on NASA's part. The driving requirement at this point seems to be cost and schedule (including schedule risk), which means avoiding any unnecessary technology development programs on the critical path. So despite the fact that methane propulsion isn't intrinsically risky, the fact that it's currently non-existent in terms of the technology-readiness level that NASA will want at the Preliminary Design Review probably assures that it won't be incorporated into the CEV, at least for the initial version. It could, however, be an upgrade later, assuming that the program gets to the point at which upgrades will occur.