I gotta admit, I started getting a little weirded out by Dr. Finn pursuing a relationship with Isaac, but they did explain it well, they've been laying the groundwork for a while, and it does make sense. Hell, there are guys in love with their blow-up dolls or babes on the Internet that they've never even met. Isaac is good to her, helps her with the boys, and in general has been a very good friend to her. He noticed when she changed her hair a little. The parallels to the TNG episode "In Theory" are obvious, and much of the rationale is the same.
Except the stakes are higher. Data's one-episode relationship with a guest star we'll never see again (which saddened me because Michele Scarabelli was cute) is not the same as two regular cast members hooking up. Dr. Finn is an intelligent, career- and family-driven woman who's a bit lonely. Heck, she hooked up with Yaphit last season. But what the hell. I got over the weirdness by the end. If two people want to hook up, and they're okay with it, then it's not my place to judge.
Also, I think it mostly worked because of Penny Johnson's acting chops. She sold it. When Isaac announced that the experiment was over and he had no more data to collect, and she said "So... you've gotten what you want from me and now you're done with me?" and it was exactly the same hurt, unbelieving tone you'd hear from any other female in that situation, suddenly I got it. Holy shit, are all guys, even artificial ones, that bad? It was real to her. That's all that matters.