Probably not in the mostly Hindu areas (India is huge), but Pakistan was made in order to have Muslims rule over the part of the former India,
"About half a million Muslims and Hindus were killed in communal riots following the partition of British India. Millions of Muslims living in India and Hindus and Sikhs living in Pakistan emigrated in one of the most colossal transfers of population in the modern era"
and the violence didn't stop after Pakistan was formed:
https://en.wikipedia.org/wiki/India%E2%80%93Pakistan_relatio...
"violent partition (...) three major wars, one undeclared war and (...) numerous armed skirmishes and military standoffs"
https://en.wikipedia.org/wiki/1971_Bangladesh_genocide
And the atom bombs prepared on both sides.
https://en.wikipedia.org/wiki/List_of_states_with_nuclear_we...
And you are absolutely right that "the only real issue most Muslims have with any non-Muslim country is that it is a general perception that they're Muslim first." Unfortunately, Islam has its political component still considered as the inseparable part of the religion.