With all due respect
1) not all minorities have their own countries. Examples today would include the Tamagzight people in North Africa and the Kurds in Iraq and Turkey. Other examples could include Christians in the Middle East (Lebannon comes to mind, but I think there are other countries as well), Uighurs in China, or even people living in a place like Iran that is a religious theocracy who want more freedom.
2) in particular, for the case of the US, there has been, since the founding of the country, a large population of African-Americans who don't really have a home country anymore, and don't really have much of a choice but to be American, because, having lived there for hundreds of years at this point, that is the only country they know.
3) I do believe that religious tolerance, and tolerance in general, pays off in the long run. Many early American colonies were founded by people seeking greater religious freedom - Pennsylvannia, founded by a Quaker, Plymouth was founded by Pilgrims who rejected the conventional dogma of the Church of England at the time. More recently, the large number of scientists and engineers fleeing the Nazis in Europe during the early-mid 20th century did have a large impact on American industry, in fact I linked Andrew Grove's wikipedia page in another post on this thread as an example.