With his explicitly Christian Christmas message. I note this after his more secular, godless recent Thanksgiving message that ticked some folks off.
President Obama, as I see it, operates in the political theological tradition of the religious left, Christian-Left ala Cornel West (though as an elected politician, Obama is far more conservative in his policy decisions than they want him to be). They are arguably the heirs to Martin Luther King's political theology. (I won't go there with Bonhoeffer; at least not yet.) In addition to being generously ecumenical, the Christian-Left types, like Obama, seem to flirt with unitarian and universalistic theologies making them like the Jonathan Mayhews of the Founding era.
Is Obama a Christian? Was Jonathan Mayhew a Christian? Are Mormon's Christian? These are all related questions.