The problem is not in being pro-India. Its their country and being pro-country is not a negative trait. The problem is to prove yourself pro-India, you need to portray yourself anti-Pakistan.
Even people at intellectual level are no exception. I would salute Khushwant Singh and Gulzar who always gave positive comments about Pakistan (though they are non-Muslims), but when you look at Javed Akhtar on one side he portray himself very liberal and come up with lines like (sarhaden insanon ke liye hain, socho tum ne maine kiya paya insan hoke) and then you see his anti-Pakistan comments.
Even when Muslims in India support Pakistani cricketers, they are doing that at risk of being called ‘fifth columnist’.
The question is here not about right or wrong decision, the question is here the mentality that developed / was imposed on Indian Muslims over the period of time.
Agree what you said. Pakistan has a narrative which is based on Islam (wrongly or rightly. That is not question here). You can expect miserable state of minorities in a religious (so called) state and there is no denial to it. But Muslims living in secular India should have a different perspective. They should not have been tagged fifth columnist, with advise to move to Pakistan, when they talk about problems in India.