When Turks left about 100 years ago Muslims were a minority but thanks to much higher birth rate they now want to set the rules in Bosnia. Serbs know that, that's why they resisted, and still resist, a unified Bosnia.
Ottoman Empire tolerated Christians, true, but to achieve anything in life you had to convert to Islam. Otherwise you could just remain a haraç-paying Christian peasant without any chance of education or growth. Haraç was a tax for being a non-Muslim.
It was super hard to be a thriving Christian under Turks. In fact the Turkish policy was to demographically and economically slowly bleed Christians and for those with ambition to convert to Islam.