In order to criticize a religion, you must understand their theology, and criticize them by it alone. And you must not criticize one religion by someone else’s theology. For example, you should not criticize Muslims by Christian theology, or Jews or Hindus by either Muslim or Christian theology. This happens a lot simply because the world is West dominated by culture, and the only theology they are familiar with is Christian theology.
Atheists criticizing Hindu theology is like them criticizing High School Science for being incorrect. High School science is presented that way because complex concepts cannot be directly conveyed, and so instead, a limited explanation is given through which one may be guided to the complete truth later.