One argument sometimes made against federally recognized civil unions by anti-gay-marriage side is actually purely political.
They worry (leaving aside whether rightly or wrongly) that this is simply a first step towards full legalization of same sex marriage, which they oppose, even if they had no problem with providing equal rights per se. In essence, they worry that the side advocating same sex marriage will pretend to agree to the "civil union" compromise, but push till full recognition once that's achieved (which would be much easier of a step at that point).
This is comparable to other concerns over previous political compromises between conservatives and progressives, such as balancing the budget (e.g. one side agrees on raising taxes in exchange for drop in spending... lo and behold, a bit later, the spending is either never dropped, or raised back, while taxes are already permanently raised); or immigration (where allowing amnesty during Reagan time was supposed to be countered with border security... amnesty was granted, border security never happened).
To put it in Middle Eastern political terms, in their experience they expected peace, but got a hudna - which is a temporary ceasefire explicitly aimed with one side (or both) intending to continue the conflict once the ceasefire ends. Strategically, that makes people more resistant to compromise and deal-making.