A trailer kind of defeats the purpose of a pontoon, IMO; if you're going to tow and store and license a trailer, get a small boat instead.
Rooftop is OK, depending on the size of vehicle, method of tying down, and the weight of the pontoon. Getting a 70# one up there can really ruin a guy's back (ask me how I know).
Ideal way is to store it in the garage overhead on a pulley, then just drive a small PU under it, lower it and go. Returning is the reverse - a 5 min task at most. 'Course that requires a PU, not a Corolla or something; just part of the decision to buy a pontoon instead of a float tube.
It's possible to split most assembled pontoons into two halves with just a couple of frame bolts and the seat removed. Makes it a lot easier to shoe-horn into a small SUV or something, and re-assembly is quick.

It shouldn't be a problem in Indiana, but be careful of transporting inflated pontoon bladders over higher passes. A 1000-ft increase in altitude means a 1/2 psi increase in internal pressure, and pontoons only carry about 3 psi, so 1/2 psi is significant. A 5000-ft pass can rupture one.