Because the leaders of HIS church--he was a VIRGINIAN--did NOT support state tax monies to churches.
Why don't you simply look on the Internet? Use a search engine, like Google. The evidence is absolutely overwhelming that Jefferson did NOT support giving state tax monies to churches:
Jefferson, pioneer for separation of church and state
WHERE DID THE PHRASE "SEPARATION OF CHURCH AND STATE" ORIGINATE?
The phrase originates in Thomas Jefferson's 1802 letter to the Baptist Association of Danbury, Connecticut. Jefferson was responding to the Danbury Baptists' complaints that Connecticut's law was oppressive to their religion (among other things, Connecticut's law allowed towns to levy taxes for the support of a religion designated by the majority of voters; since Connecticut was overwhelmingly Congregationalist, the law effectively forced Baptists throughout the state to support Congregational churches). The Baptists, who knew of Jefferson's advocacy of separation, "honored [Jefferson] as an apostle of religious liberty. Much of their address sounded like [Jefferson's] bill for establishing religious freedom in Virginia, and they hoped that the sentiments of their 'beloved President' would prevail so that 'hierarchy and tyranny' would vanish from the earth" (Dumas Malone, Jefferson the President: First Term, 1801-1805, p. 109).
The man COINED the phrase "separation of church and state" for God's sake!