The church with which he was naturally affiliated was the Presbyterian. The most eloquent preacher of that denomination was the Reverend Dr. Palmer of New Orleans, who was an aggressive champion of slavery as a divine institution. His teachings were feebly echoed in thousands of other pulpits. Now Lincoln abhorred slavery. He incorporated human freedom into his religion...It may therefore be seen that the church did not give him a cordial invitation. If this needs any proof, that proof is found in the fact that the pastors in Springfield voted almost unanimously against him...
...this did not embitter him against the church...all his life long he kept up such bonds of sympathy with the church as were possible. He bore with the faults of the church and of ministers with that patience which made his whole character so remarkably genuine. He was a constant attendant at the services, he was favorable to all the legitimate work of the church.Here is a sermon from Dr. Palmer, along with an address from another prominent clergyman:
Thanksgiving Sermon, Benjamin Morgan Palmer, November 29, 1860
A Southern Christian View on Slavery , James Henry Thornwell, 1861
Of course, those views are in the past. Here are a couple of apologies for past positions:
The Southern Baptist church apologized for their stance on slavery in 1995.
A New Orleans Archbishop apologizes for slavery Feb 1, 2011