In his own words- religious toleration:
"Well aware that the opinions and belief of men depend not on their own will but follow involuntarily the evidence proposed to their minds; that Almighty God hath created the mind free, and manifested his supreme will that free it shall remain by making it altogether insusceptible of restraint; that all attempts to influence it by corporal punishments, or burdens, or by civil incapacitation, tend only to beget habits of hypocrisy and meanness, and are a departure from the plan of the holy author of our religion, who being lord both of body and mind, yet chose not to propagate it by coercions on either, as was in his Almighty power to do, but to extend it by its influence on reason alone; that the impious presumption of legislators and rulers, civil as well as ecclesiastical, who, being themselves but fallible and uninspired men, have assumed dominion over the faith of others, setting up their own opinions and modes of thinking as the only true and infallible, and as such endeavoring to impose them on others, hath established and maintained false religions over the greatest part of the world and through all time...."
Aside from being the longest run on sentence ever, that seems like a nice sentiment.
Jefferson deserves much more criticism than he gets, but deserves praise for this.
Before the civil war, various colonies in America were set up as enclaves for one religion or another, and to insist that the new nation simply tolerate it's various religions was an idea at the time that would have been considered unpopular on almost a John Adams level.