Dear internet rando. The reason I criticise Hinduism more than other religions is the same reason a Pakistani atheist will criticize Islam more or an American atheist will criticize Christianity more. Different religions occupy different positions in different societies.
Yes all of them are irrational. And yes irrationality should be criticised everywhere. But when your village is near a forest and it's full of tigers, you don't set traps for mice. Your response to religion has to be based on the most popular flavour of it in your locality.
If you're of the view that Indian atheists should criticise Islam and Christianity more than Hinduism, then the logical follow-up to that is that Western atheists should focus all their attention on Hinduism too. That'll be out of balance, won't it? Understand power structures.
Modern atheism is about criticising religion, yes. But it is also about demonstrating that religious authority itself is a bad thing and that it convinces good people to do bad things. And authority comes from different sources in different places. Get that into your head.