Communists, meaning people who were members of the Communist Party or identified as Communists and associated with other Communists, were more likely to have come into contact with Soviet agents and been persuaded to spy or subvert US aims. We are talking about security risks not security certainties. It's entirely reasonable to remove risky people from sensitive positions. Any organization that failed to do so would fail to achieve the objectives given to it through the democratic process; it would serve another master. This is entirely separate from the question of who should choose the objectives of the government.
Ironically, Communists wished to overthrow the US government and were anti-democratic.
Ironically, Communists wished to overthrow the US government and were anti-democratic.