It just makes sense logistically. Lots of buildings not in use during business hours that have adequate parking and plenty of room for people to move around and stand in line.
It's not like they are having religious services or preaching to the voters while the polls are open.
Also, in the biblical New Testament sense, the building itself isn't really the "church". The church is the people that gather together.
"In the New Testament, the ekklesia. In the Bible, this has no reference whatever to buildings or organizations but to the called-out assembly, the covenant people of God. In the overwhelming number of cases, the church or ekklesia of both the Old and New Testaments is the visible covenant community in a particular locale or region." Source:
Glossary of Frequently Used Terms
Now if each "church" or assembly of worshippers was imposing their beliefs on those waiting in line to vote, then we would have an issue of church and state not being seperated but if it is just a matter of using a very convenient building, I don't see how that would be a problem.