The LOR could have hurt if you thought it was a weak one...usually the apps require three though, so if your other two were stronger and from history, then I wouldn't sweat that too much (my third LOR was a non-history prof as well). Not knowing much about you or your experience (or whether you applied coming out of undergrad or from a masters program), another suggestion would be research experience...have you done archival research and did your writing sample demonstrate that? Also, honestly, I think this year's admissions process was pretty much a crap shoot...I applied to 8 schools and had a 50% success rate...I was accepted by a school that I thought I had no chance of getting into and was rejected by some ranked lower. Thus, another suggestion would be to apply to A LOT of schools...sometimes its simply about probability...boost your chances with a longer list of schools. Fit also matters though. After surviving the cycle this year, I'd say that this is the NUMBER 1 factor for admissions...there are going to be a lot of great applicants, but how you sell yourself and convince them that you belong at their school will set you apart.