There is more than one rapture, one taking away.
Matthew 24:40-41 is not the rapture of the church but is the rapture of the evil people to hell at the time of the 2nd coming.
You see, only the righteous are allowed to enter the millennial kingdom.
Its all about context. Matthew is talking to the Jew in the tribulation period here. The verses preceding Matthew 24:40-41
talk about the 2nd coming followed by this next event.