I think (especially with all the Danny/Lindsay action lately on the show) that Flack would be a really bad friend to Danny if he and Lindsay started going out. I prefer FM to DL, but I wouldn't want Flack and Danny's friendship to be wrecked over Lindsay.
For me, the Don/Lindsay/Danny love triangle is a very complicated and intricate one. I mean, you have Danny -- a very emotional guy, who takes things very seriously and (although he tries to get people to think the contrary) cares deeply about the women he's with and gets attached. He has the rep of a player, and maybe he is, but he just can't find the right girl. He likes Lindsay, because she's his character foil; city boy, country girl. Whereas Danny's emotionally unstable, a constant rebel to authority, and his secrets are dark and out in the open, Lindsay's pretty much the opposite. She's sweet, smart and determined; when she gets something wrong, she accepts it and proves that the other person was right. She has her skeletons but she keeps them quiet. She doesn't really like Danny, mostly because he's too unpredictable. She needs someone stable in her life.
Flack is more stable. I don't think I've ever really seen him lose his temper or become as emo as Danny on the show. Flack of course has his own shadows. While he's definitely a good friend and the shoulder you lean on ("All Access" S2, "On the Job" S1), we saw that taking down his mentor Gavin Moran was hard on him ("The Fall" S1). He definitely internalizes things, probably because he thinks he has to be strong for everyone else. He also dodged a question about his father, dubbed an "NYPD legend" by Moran. It's my belief that it's because Flack's trying to make a name for himself and trying to outrun the shadow of his father.
Lindsay doesn't seem to be that close with her parents either, as evidenced by the conversation she has with the father of the victim in "Stealing Home" (S2). It's one thing she and Flack would have in common. Maybe it would be something that would draw them together. Also, Flack seems to be the hero type. With Lindsay and her dark secret, he'd probably want to help her. She wouldn't want to let him at first, but she'd eventually let him in. Lindsay strikes me as the helper type as well -- Flack needs someone to worry about him, and Lindsay could do it. Would do it, just because she felt it was the right thing to do. Because he needed it.
Personally, I think Lindsay's comment in "Love Run Cold" (S2) about having issues to deal with, things she thought she had gotten over but she really hasn't, could be about anything. I choose to take it as it's about Flack. Could it be that during the end of S2/off-season they got closer and she fell for him, so hard that she pushed him away? Now that he's back on the job, she sees him more often. Lindsay thought she had gotten over him, but she really hasn't.
Flack is Danny's best friend, as we've seen throughout all three seasons so far. Danny's gone to him when he's felt that the world turned against him ("On the Job" S1), when Louie was beaten up by Sonny ("Run Silent, Run Deep" S2), and Flack was stability when Danny was a wreck after Aiden's death ("Heroes" S2). I'm sure there's tons more. The point is, I'm pretty sure that there's nothing that could ruin a relationship like that, even a girl. There would be some distance for a while, and maybe they'd even fight it out. But afterwards they'd just have a talk and then they'd play some hoops on Saturday, because that's what best friends do.
Sorry for the novel!