The question is worded in terms of morality, not acceptability within society. I might find non-veganism immoral, but I rarely mention this fact to others, and while I have lived a vegan lifestyle for almost 7 years now, I make no suggestion to others on the subject unless prompted directlt in conversation. If many Republicans feel that same-sex relationships are immoral, this may primarily impact their attitudes towards their own lives and not how they see those of others.
Furthermore, less than 50% support doesn't mean over 50% direct rejection. Plenty of individuals don't know what to think and will let anything happen as they drift through their lives. Thus, this statistic alone isn't enough to conclude that most Republicans are against same-sex relationships.