No, the minimum franchise tax you refer to (not alternative minimum tax, a completely different tax) does not apply to every company in the state. In particula

No, the minimum franchise tax you refer to (not alternative minimum tax, a completely different tax) does not apply to every company in the state. In particular, it does not apply to non-profits with exempt organization status, which are what people generally think of when they think of non-profits. While my experience is with exempt organizations, my understanding is that the non-profits it applies to are non-exempt non-profits, such as homeowner's associations.