Roosevelt was a notoriously tricky guy when it came to people he trusted and didn't, and he didn't trust Truman. We don't have any more insight into his motivations; he never wrote them down or told anyone. One can speculate (Truman had tried to audit the Manhattan Project as a waste of funds several times when he was a Senator, maybe FDR worried he would cause a stink), but really, we don't know.

As for Congress: yes. Seven Congressmen were told about it by March 1945: the Majority and Minority Leaders of the Senate and House (Barkley, White, McCormack, Martin), the Speaker of the House (Rayburn), and the Chairman and Senior Minority Members of the Senate Committee on Appropriations (Bridges, Thomas). These groups were told so that Congressmen (like Truman himself, earlier) who were snooping into war waste and fraud could be easily told to stop, and to make sure no questions were made about large War Department Appropriations towards this secret project. There were several Congressmen (including Truman) who had heard rumors about the project, but they were not catalogued or given more information.

One more thing on Truman. In 1943 as I mentioned he tried to investigate the project at Hanford (where plutonium was being produced) as the head of the Senate Committee to Investigate the National Defense Program. He was told (three times) by the Secretary of War, Henry Stimson, to drop the investigation. (Stimson to his diary: "He threatened me with direct consequences. I told him I had to do just what I did. Truman is a nuisance and a pretty untrustworthy man. He talks smoothly but he acts meanly.") He agreed to drop it. But in July 1943 he wrote to a judge in Spokane, Washington, regarding Hanford: "I know something about that tremendous real estate deal, and I have been informed that it is for the construction of a plant to make a terrific explosion for a secret weapon that will be a wonder." So he got wind of some rumor, but didn't pursue it. Though he did tell a judge — which is exactly why the Army et al. did not want to tell Congressmen; they can be indiscreet, and are hard to punish for their indiscretion on the basis of their position.