@Justin,
Welcome Tsamaya!
Jefferson's "wall of separation" is supposed to address the underline issue of
the complete separation of religious matters (which Jefferson thought was deeply personal) and Governmental forces (which he thought should have no say in private affairs.) Jefferson was very revolutionary and got some bad slack for that thought. But without that caveat... the
establishment clause would have perhaps not have been included in the U.S. constitution. Basically, without the "wall of separation" clause, it would be like the government
legally telling you what and how to worship.
But please do start a separate thread on the topic in the philosophy of politics section. There is a lot of information on the subject I think you would find it very fascinating and the historical instances that substantiated Jefferson's thoughts interesting as well.