Civil unions, while a vast improvement over the absence of any recognition of same-sex relationships, are almost by definition second-class arrangements.
The temptation is to think that Obama knows this, and that his reluctance to endorse marriage equality is more political than personal. When he ran for the presidency in 2008, it was the conventional wisdom that supporting gay marriage would be politically fatal. With shifts in public attitudes, that probably will not be the case in 2012. According to the Pew Forum on Religion and Public Life, 42% of adults now favor same-sex marriage, compared to 37% in 2009. The trend seems clear.