It's not as modern as you might think, just for a long time the Catholic church dominated all kinds of Christian doctrine and executed anyone who questioned it as heretics. Even early Protestantism was still very much Catholic in their doctrine. But there were always people who dedicated their lives to studying the Bible as independent scholars.

Besides you can find examples in other parts of the Bible of believers going to be with God in their physical bodies:

• Genesis 5:21 When Enoch had lived 65 years, he became the father of Methuselah. 22 After he became the father of Methuselah, Enoch walked faithfully with God 300 years and had other sons and daughters. 23 Altogether, Enoch lived a total of 365 years. 24 Enoch walked faithfully with God; then he was no more, because God took him away. - for everyone else in that genealogy it says they died, Enoch was the only one who was "no more" because "God took him away".

Elijah was another man who did not die but was taken by God in his physical body:

• 2 Kings 2:11 As they were walking along and talking together, suddenly a chariot of fire and horses of fire appeared and separated the two of them, and Elijah went up to heaven in a whirlwind.

Moreover, Elijah's return is prophesied "before the coming of the great and terrible day of the Lord,". (Malachi 4:5)

You honestly have to allegorize massive parts of the Bible to think that it doesn't talk about physical Second Coming of Christ or the possibility of believers being taken up to be with God in their physical bodies.