FundAfter is a Christian company (think Chick-Fil-A and Hobby Lobby), and so we operate by a certain set of values (and in beta, are only accepting certain kinds of projects).
Kickstarter is also a company that operates by a certain set of values. They’ve come out in support of some things we don’t:

LGBT propoganda
Genderless bathrooms
Death of the unborn

And now, Kickstarter is officially a “Public Benefit Corporation”–which means that a certain percentage of every dollar of profit will be spent supporting causes like these. If you don’t believe me, check here, here and here. In a nutshell, we don’t support Kickstarter on moral grounds.
However, there’s another great reason to skip Kickstarter: They actively interfere with your projects and goals to push their personal agenda. I believe that Crowdfunding should be a tool to use, not an editor/censor/wealth-redistributor. Kickstarter wants to build a community, and to control it.