Chess.com has made several statements on the current conflict:
https://www.chess.com/article/view/on-the-invasion-of-ukraine#flags
https://www.chess.com/blog/CHESScom/in-support-of-ukraine
You are free to think whatever you'd like. However, Chess.com has made this decision, and you should respect it, even if you think differently.
Everyone with a sense of right and wrong knows that invading a country is wrong. If the purpose of greying out Russian flags was to be anti-war chess.com would grey out American flags every time the United States invaded a country. By greying out Russian flags chess.com is admitting that war is okay so long as the [removed -- MS] States of America isn't doing it.