Oh, I definitely think we're still meant to love them - she certainly seems to; apparently killing Sirius off was awful for her, she loved Remus and had him as a metaphor for AIDS patients who were discriminated against, and she gave Harry James's patronus. But I think she also wanted them to essentially be tragic heroes, good men who were nonetheless taken down by their own flaws. And yes, I think distrust was a huge part of it - the trio has some of that, but they're able to come back from it before it's too late.