You cant stop at verse 39, you must continue on to verses 40 and 41.
The point of Jesus teaching there is not that everything that happened in the time of Noah, will happen during the 2nd coming ...
His point is that there is a coming judgment that will happen upon His second coming, not that the signs will be the same. When Christ comes again, He will separate the "wheat" from the "chaff." ... Verse 40 and 41 talks about one being taken away, and another left. Some Christians mistakenly teach this is a reference to the rapture. It is not. It is a reference to Christ taking away unbelievers into judgment at his second coming. ... Think about it for a minute. In Noahs day, who were those taken away by the flood? UNBELIEVERS. ... Just as in the days of Noah, unbelievers were swept away into judgment, so shall it be when Christ returns. One will be in the field, and one will be taken ... they will be taken away into judgment, and only believers will be left on Earth at the beginning of the millenium.
It's obvious you will twist whatever verse I point out to fit your beliefs. I don't have the time to point out all the differences in the two events. If you have the time, please read this article: http://www.christiancourier.com/archives/matthew24.htm
God Bless.