She was essentially a decent person, with a conscience, that's why.

She was not his mom, but when he got kidnapped in the fake kidnapping I thought Jed was his mother, she was actually screaming something like "take me! Take me instead!" Then when I realized she was not his mother and remembered that she had a child of her own, I found her reaction a bit over the topOK, she loved Danny, but in that scene she freaked out too much, like he was her own kid..so it was confusing.
"Please, if you are trying to convert me, this isn't a good time"

You're welcome.
I have actually seen it from beginning to end twice. And then watched reruns of a couple of the episodes a third time.
I found it to be very confusing the first time around and some things did not make sense. I also got confused about a couple of the characters. Once i knew the story from beginning to end, a second watch gave me the opportunity to catch things i had missed the first time around. But even after watching it twice, i still find some gaping plot holes are a bit of a distraction to the overall story.
I have not read the book but did read in reviews that the ending of the show was different than the ending of the book. A quick look on Wikipedia revealed the book ending, which i thought would've been much more satisfying than the ending on the show.
Fraaaank. FRANK! Get my jean bin. Susie wants my jeans.
No she doesnt.

Thank you very much! You caught a lot more details than I did. I'll probably watch this series again, as I enjoyed it so much.
I may read the book that it's based on, 'cause I'm curious about what made the Pine character such a recluse. Yes, we hear vague mutterings about his war experience and losing his father but there seemed more to it than that.

No she isn't his mom. At some point one of the characters mentions that Danny is visiting his father for the summer and then goes back to his mom in NY.
I think that Danny and Jed are close because he misses his mother and she misses her son who is living with her sister. Also because both of them are essentially outsiders in Roper's world.
Roper treats her very well (at first) and for all appearances they seem to be in love. But i didn't get the impression they've been together that long (maybe a year at the most if that).
Even though she's his girlfriend, she comes in second to his business dealings, and so does Danny. Roper doesn't even go to the airport with him when he's leaving because he's dealing with a work issue.
There are probably long stretches of time during the day when Roper is busy and Jed/Danny spend time together keeping each other company and filling the void that each has.
There's a great moment in the kidnapping scene when Pine tells Dan to run to his mother. Pine knows all the details about Roper and everyone around him. So it was intentional that Pine mentioned Danny's mother rather than his father. I thought it was very clever of him.
Fraaaank. FRANK! Get my jean bin. Susie wants my jeans.
No she doesnt.