The new giant Salvation Army sign outside doesn't help, does it?
I was talking to their coffeehouse manager a while back and found out a few things. (I brought in a group of teenagers to hear about the work they're doing)
They operate as a volunteer-run, non-profit coffeehouse, but
their profits don't go to the SA, they go to everything from local community projects to international relief work, etc. The volunteers who run the coffeehouse don't necessarily have any religious connection or faith background at all, or connection to the SA at all
Where the money goes impressed me quite a bit. Even though I have a clear faith background myself, I respect them not just funnelling things to their own channels or faith organizations, but to projects that no matter what one's background is, you can consider it a worthy cause. It's also given to several types of charities with diverse purposes. The common thread is non-political, non-controversial initiatives that focus on caring for people, communities, the environment - real stuff that almost anyone can get behind. The care for the environment also impressed me (although I'm not sure why they still use foam cups despite of this

)
A church meets there Sunday nights and I believe another one rents their space Sunday mornings, so that's why they're not open Sundays. I think the shorter hours as of late is mostly due to lack of volunteer time.
My only irritation with FRWY is that although they have great fair-trade stuff, they do espressos, but not cappucinos or lattes. I can make coffee at home, but I don't own a $400 espresso machine!.

I'm sure it's a cost issue and/or the difficulty level for the volunteers though. At least they always have soy and honey out, which a lot of coffee shops cheap out on or keep behind the counter.