Personally as an Athiest, I oppose any mixture of church and state. I do believe that unfortunately it will be a long time before my religious beliefs are respected by a majority of the population.
However Rick Warren is actually much more progressive than many of the previous speakers selected to offer the inauguration prayer. I fully understand some of the pain members of the LGBT community must be feeling as a result of Warren's unfortunate statements defending traditional marriage by stating that gay marraiges were almost an equivalent of incent and child abuse. Warren definitely mispoke, and unlike almost all leaders of the evangelical community in the past 20 years does have gay friends and acquaintances and does not "damn people to hell" like many of the fundamentalist preachers of old.
Obama is as fully committed to the cause of gay rights as Clinton, and hopefully this is some strategic posturing that will allow segments of the evangelical community to not challenge a repeal of don't ask don't tell, and maybe make civil unions a nationally protected right. I have no opposition to gay marriages whatsoever, but it will take a generation before we are able to consistenly make gains at the polls against anti- gay marriage ballot iniatives.
I feel the same way my friend. I wouldn't call myself an atheist as I don't know if god exists or not (and frankly even if s/he existed, I wouldn't worship him/her), but I am often disappointed with the role the church has in how this country is governed.