I think it's probably more to the structure of the denominations themselves. Like Catholicism, central to Mormonism is the central authority of the church, including priesthood authority. Most Protestant denominations, predominant in the US, are not nearly as rigid in their beliefs regarding priesthood authority, centralized authority, or even a set dogma. If your local Baptist/Lutheran/Methodist church isn't tolerant of certain beliefs, or you don't feel comfortable there, it is relatively easier to just start up your own church. In Mormonism (and Catholicism), this doesn't happen, because the centralized authority of the church is a key piece of the doctrine. For Protestant denominations, they largely reject this central authority, so they tend to be more fluid on these topics. In regards to race, this wasn't an issue with the Catholic church, but with other topics (say, celibacy of priests), there aren't "we maintain the legitimacy of the Church in Rome but our priests aren't celibate" type denominations popping up much.
I suspect this is why, even though there was much by way of explicit prohibition of races in many churches throughout the US, most churches seemed to have ended up segregated anyways.