Could someone explain to me what the legal difference between civil unions and marriage for same-sex couples is in the United States?
Main legal difference is recognition I believe.
There has been no compact for states to recognize other states' civil unions like there has been for marriage (in addition to making the federal government not recognize any same-sex marriage, the federal DOMA law also said states can choose to avoid to recognize other states' marriages if it is between a same-sex couple) and there are many federal legal rights and benefits (such as spousal/survivor Social Security benefits) that civil unions will not confer unless the statutes are rewritten to include civil unions.
http://en.wikipedia.org/wiki/Rights_and_responsibilities_of_marriages_in_the_United_States