Jefferson very much wanted to win over to his Republican cause all those ordinary religious people who had voted for his opponent. To do so he knew he had to offset the Federalist accusations that he was an enemy of Christianity. Consequently, to the surprise of many Federalists, he had good things to say about religion in his first inaugural address. He also knew very well that effect he as president would have when in January 1802 he attended a church service held in the chamber of the House of Representatives. His attendance attracted wide public notice and astonished the Federalists. Even though other churches were available, Jefferson continued to attend church services in the House chamber and made available executive buildings for church functions. Sometimes the U.S. Marine Corps Band supplied music for religious services. As president, however, Jefferson held to his vow never to call for any days of fasting and prayer as his two predecessors had done.Empire of Liberty, pgs. 586-87. Now, as Wood points out, Jefferson did all this because he was trying to woo the mass of voters who were attached, with varying levels of devotion, to Christianity. And there were limits to how far Jefferson was willing to pander -- he did not, as the end of the quote above indicates, call for national prayer and fasting on notable occasions. However, Jefferson was quite willing to use federal facilities, and hence federal funds, to support public Christian worship.
It was also around this time, according to Wood, that Jefferson began to work on his redaction of the Gospels, a work commonly known today as the Jefferson Bible.
As with most things involving Jefferson, he was not incapable of being duplicitous in order to get what he wanted. Hypocrisy is the tribute vice pays to virtue, after all.
Related item: don't forget Jefferson's letter to the Ursuline nuns upon taking over the Louisiana country. He promises those nuns not just the protections of the Constitution, but the "patronage" of the U.S. government. Here's a copy of the original letter, still treasured by the Ursuline religious community in New Orleans. On an unrelated note, Jefferson had terrible handwriting...