No.
How about the chess club?
Yes.
Why should my tax dollars fund a space for either or any of them?
Chess is an legitimate academic pursuit. Worship (or the degradation of worship in the case of the atheist club) is not. The purpose of the school is to educate, not to indoctrinate.
Therefore!
Get government out of the education business. Begin the process of privatizing K-12 schooling. Let these non-neutral cultural, political, and religious worldview issues be settled in the private sector between private teachers and private principals.
You seem to be under the impression that the school is sponsoring the FCA group. It is merely using the building. Have you ever been to a school building in the evening after school hours? It is a busy place, many groups are using it and not all are school sponsored teams, clubs, etc.
Even churches can rent the space to use for worship on Sundays, that doesn’t mean the school is sponsoring the church. Our church rents the gym and a couple of classrooms to use for Wednesday night kids programs. Using space is not the same as sponsoring. It is a public building and after school hours it is used as a community center for all kinds of groups.