How did this happen? Simple.

Fluttershy accidentally took the wrong train while on vacation and wound up in a small town filled with many creatures. While she knew that this wasn't where she wanted to go and that she had to go back, she was also in awe of all the talking animals in that town and thought that she'd introduce herself to some of them. Because none of them have seen Fluttershy before, they brought her to meet the mayor and secretary so she'd feel more at home while she was there. That's how she met Isabelle.

After their initial meeting, Isabelle and Fluttershy hit it off. One thing led to another, and soon the two of them were an item. Fluttershy kept in touch with Isabelle after she went back to Ponyville via letter, and their feelings grew with every letter. Fluttershy took the train to Isabelle's hometown whenever she wanted to see her in person and eventually moved there after a lot of thinking. She misses her friends in Ponyville, but she's happy about the choice she made.

And then Butterscotch came along, who was actually the result of a wish. Isabelle and Fluttershy were watching a meteor shower one night and decided to try and wish for a child on one of the shooting stars. They've been talking about starting a family for a while, so they thought that they'd try their luck. And it worked! The next morning they woke up with a newborn foal-puppy asleep in their bed and named her Butterscotch.

TL;DR Fluttershy and Isabelle met after Flutters took the wrong train and fell in love, then wished for a baby on a shooting star and it somehow worked.