It makes me really angry at your professor, and I don't even know you. That is so incredibly rude! Our professors always say that if you ask for a LOR, they will tell you very up-front if they feel they can't write one, or if there is something impeding them from writing a good one. One prof of mine even went as far as to say that she had a student that she absolutely loved, almost like a daughter, but when she asked for a LOR she had to tell her no because the girl just wasn't that great of a student.
So, I'm not saying you're a bad student or anything of the like. I'm just saying it makes me angry at your prof.
It's just an unlucky thing to have stuck in your file. I don't think it's going to make or break all of your decisions, though.