You like many people say that but do understand what it means.
A big company wants to build a theme park and gets development money from the state.
A church wants to build a theme park and gets development money from the state.
That is okay because both are treated the same.
If only the church or only the commercial company get money then you have a failure of separation of church and state.
And just so you understand this is the exact wording in the constitution
""Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof ..." and Article VI specifies that "no religious Test shall ever be required as a Qualification to any Office or public Trust under the United States." "
In other words the original intent allowed states to actually have state religions. It only restricted the Federal government and even those restrictions are very limited and DO NOT LIMIT WHAT A CHURCH CAN DO! Some states have also embraced the separation of church and state but all those laws would make it illegal to exclude a church from receiving the same breaks that a non-church entity does from a state.
It is not a law to protect you from religion or to restrict religion. It is a law to protect the church.