Rye just gets taller than wheat does.  Period.  And that is why it is more susceptible to lodging. 

I concur with Kyle - put the rye on poorer ground if you can. Expect lower yields.  You can't push the nitrogen on rye like you can on wheat, due to lodging. 

I would consider trying to use a growth regulator on rye, but I am pretty sure it is not labeled (legal),  so I won't do it.   :)

edit: if you are not aware,  rye will head out earlier than wheat, but the grain will be ready to harvest after wheat is harvested.