I believe that the longer your trip the more you should pay, but consider this:
Transit ridership in the suburbs is poor compared to transit ridership in the city. If we want to encourage more people to take long distance trips by transit, then we need a fare policy that encourages that.
Not everyone can afford to live close to where they work, so its not equitable to only reward people who can afford to live a "short commute" lifestyle. Strict fare-by-distance fails from this perspective.
We shouldn't have fares double, but we should have gradual increases. Also, fares should be the same within municipal boundaries. You should be able to travel anywhere within your city for one flat fare - again, out of equity.
I propose that we keep the fare zones we have now, reduce the fare to cross the border to a single dollar, and give you X hours of unlimited travel (with a fresh X hours when you pay the dollar upgrade).
Alternatively, we can move to a fare-by-time scheme, where one fare gets you X hours of travel anywhere, and the next X hours is charged.