He probably reflected on the fact that nothing on Earth is truly eternal... and as long as people wish to inflict their religious beliefs on others, and as long as governments have power, then there will be religious people who use the power of government to inflict their beliefs on others. It is the triumph of the U.S. Constitution that it has so far put up a good fight against those never-ceasing and dangerous movements.
TJ most assuredly believed in God, i.e., the God of Moses. Where he had doubts, I believe, was in man's behavior towards God and His laws.
Is it any wonder our nation's two greatest Presidents were lovers of the land, (and horses), who chose to live on mountaintops.
You're not being honest with yourself dayglored.
As I've mentioned elsewhere, the Bill of Rights was flawed with respect to the 10th Amendment not having any checks. The post Civil War 14th Amendment was intended to check the 10th, the 10th likewise checking the 14th. The problem is that crooked secular judges are now taking advantage of widespread constitutional ignorance by ignoring the 10th so the 14th essentially has no checks.