First: Ben Stein is obviously attacking the ideological content of the song, and by extension not only those who agree with it but also those who would use Darwinism to advance social and political agendas. Obviously the attacked aren’t going to care for this; if legal remedies can be found, they’re going to use them.
But that leads to the second point: what Lennon’s heirs and assigns are trying to do is to use intellectual property laws to stifle political and ideological dissent. This isn’t new either, but the use of copyright to do this is really scary if you think about it. It’s something that each and every one of us who expresses themselves on this and other media–especially on controversial topics–have to think about all the time. Fortunately the Stanford Law School’s Fair Use Project is going to bat for Stein. (I find it hard to believe that he didn’t consult his attorneys before inserting "Imagine" into the movie.)
It’s also intriguing to speculate whether or not this suit would have been brought if a movie more favourable to Lennon’s idea had used a portion of the song.