I know everyone wants to say this so I'll go first....
stop driving in the rain.
Seriously? Use a strip of paper (or similar) and shut the door on it - try pulling the paper through the seal. Do this all around the edge. When it comes out easily you've found the 'hole'. If the hole is in one particular area as opposed to being right down one side, you should be able to adjust the seal at that point (put something under it to make it stand proud perhaps?).
If it's all the way down one side then the door may need realignment.