Matthew 13:30 I will say to the reapers, Gather ye together first the tares, and bind them in bundles to burn them: but gather the wheat into my barn.
Jesus was teaching the Jews and what He was teaching them is exactly what they expected to hear. That is just how they expected things to turn out when Messiah comes to set up the Kingdom. He will first gather the wicked as you point out.
But that takes no cognition of the famous parenthesis, the gap in between which is the church age which the Jews did not have any understanding whatever.
Before this time of gathering God was to draw a people from the Gentiles for His name, they would be His people among the nations, the Jews would be diminished.
Now the need for the rapture becomes crystal clear for this people who are among the nations must be gathered out from the nations before God's judgement begins.
In the case of Noe he was obviously gathered into the ark before the flood arrived.