Megan Mcardle in The Atlantic quotes Orin Kerr at Volokh Conspiracy:

There's an interesting analytical similarity between the DOJ's position on DOMA and the Bush Administration's reliance on its Article II theories. If you look at AG Holder's reasons for why DOJ won't defend DOMA, it is premised on DOJ's adoption of a contested theory of the constitutionality of laws regulating gay rights. The letter says that "the President and [the Attorney General] have concluded that classifications based on sexual orientation warrant heightened scrutiny and that, as applied to same-sex couples legally married under state law then, from that perspective, there is no reasonable defense of DOMA." This theory is not compelled by caselaw. Rather, it's a possible result, one that is popular in some circles and not in others but that courts have not weighed in on much yet.