Roosevelt had entered into an alliance with the Soviet Union to help defeat Nazi Germany. In the closing stages of World War II, the Soviets had become increasingly dominant in Eastern Europe. They had boots on the ground and, through their Communist proxies, were in the process of building puppet regimes.
At the Yalta conference, FDR acknowledged the new realities on the ground by ceding the Soviets a defined sphere of influence in Eastern Europe. This led many of FDR's Republican opponents to accuse him of appeasing Stalin and, by extension, Communism. But with the Soviets already in effective control of much of Eastern Europe, and with Russian forces rapidly making inroads into German territory, one could argue that FDR had little choice but to accede to Soviet demands. The war still hadn't been won, and so it was imperative for the Allies to maintain unity until the job was done.
Had FDR lived into the post-war period, however, there seems little doubt that he would've adopted a similar approach to his successor, Harry Truman. Not long after the war ended, Stalin proceeded to go back on the undertakings he'd made at Yalta regarding democracy in Poland. This would've demonstrated to FDR that the Soviets couldn't be trusted and that, what's more, they were determined to spread Communist ideology throughout Europe. As an avowed internationalist, FDR would almost certainly have sought to contain the spread of Communism by offering economic and political support to the fragile democracies of Western Europe, as Truman was to do under the Marshall Plan.
The stand-off with Communism would not have been the same for FDR as the struggle against Fascism, not least because direct armed confrontation was out of the question due to the Soviets having atomic weapons. However, a similar moral imperative would undoubtedly have been at work. He was never under any illusions about the true nature of Communism; he only joined with the USSR as part of a strategic alliance to defeat Hitler. But with the war won, it's almost certain that Roosevelt would've recognized the clear and present threat that the Soviets posed to America's strategic interests—especially in Western Europe—and would've acted accordingly, containing the spread of Communism through the support of liberal democracy.