The primary reason for that shift is that the humanist-dominated courts, media and politicians have redefined that term. When Jefferson coined the phrase in a letter to Baptists he meant that Church and State were separate entities which should be run by and supported by their respective members. Today that term has been twisted to mean that religious and moral values should be divorced from government. Christmas mangers and Christmas carols are banned in most public venues.
Government schools teach evolution as a fact and bar any presentation of the creation position.
I am a fundamental Baptist and believe strongly in Separation of Church and State. In fact, it is widely taught as a Baptist distinctive. I do NOT support the secularization of our government, the shunning of Biblical values by most in government or the use of tax-supported institutions to promote humanism, sexual perversion, abortion, and other sovial and moral evils. I know people who take great pride in their home schooled children and those children are well above grade level. Unfortunately, because of the adamant refusal of parents who want to home school, to agree to much if any regulation of same, the concept is mostly used as an excuse for legalized truancy.