I've done it all ways, and I don't think there's a right answer.
It seems Pros aren't put off by larger entry fees. Most expect to win their entry back, and many expect to win more than their entry. So they don't expect to lose money, and the higher the fees, the more they'll win.
Common around here is one entry for Pros, a lower one for Ams. We've also tried scaling to a lower entry for lower Am divisions, with the notion that they may be more hesistant to play, and more willing if the entry is smaller.
We've also done the same entry for all divisions. I don't know how the players liked it, but it made registration and bookkeeping a bit easier.
Ultimately, I've sat in a lot of meetings for tournament planning, and we're never quite sure what the entry fees should be. It's always our best guess as to what will go over best with the most players.