This is an old thread, but the question is the same exact one I had this morning. The comments already on this thread aren't helpful, but I was able to piece together a solution. So I want to share because I don't see this question stated clearly anywhere else, nor do I see any solutions to this question stated anywhere else.
When you make a Visualforce template, you associate it with an object.
In this case, let's say your associated object is called "Trump Is Evil"
And let's say that within that object, you have an email field called "Custom Reply To Email" and that is the field you want to be the "ReplyTo" address.
Then your Visualforce template will look like this: