“They present themselves as a religiously neutral organization.”
Personally, I don’t think it’s possible for an organization that helps people find a new derech to be “religiously neutral”.
When I first heard about Footsteps, I spent some time reading their web site. There was an event posted there, and it was specifically stated that both Kosher and non-Kosher food would be provided. Since there’s no reason why even a non-observant Jew “needs” non-Kosher food, that was an obvious sign of the organization’s mindset.
Meanwhile, this topic wasn’t about Footsteps. but a halachic alternative, such as the existing Project Makom.