Barry could use his super - speed to quickly track down Zoom's lair. Once he locates it, he might try to create a distraction to draw Zoom away from Caitlin, allowing other members of Team Flash, like Cisco or Wells, to sneak in and free her. Cisco could use his powers to open up portals or disable any security measures that Zoom has set up.
Zoom could be kidnapping Caitlin simply out of his twisted sense of power and control. He enjoys causing chaos and fear, and taking someone important to Barry like Caitlin is a way to assert his dominance. Also, in the context of fanfiction, the writer might be exploring a scenario where Zoom has some personal vendetta against Caitlin that was not fully explored in the original series. For example, he could blame her for something that happened in his past, even if it's a misdirected blame.