Getting back from Nizwa to Muscat was easier than we thought. We had tried to arrange a ticket in advance on the government run buses, but apparently it’s not possible to buy tickets in advance for a trip like this (i.e. where you start at a non-originating point). We ended up lucking out and getting a mini-bus that went directly to Muscat. In addition, he stopped to let us pick up our bags which we had left at the hotel for the day. The mini-buses charge per person (I forget how much, but it was basically free), and although it started out full, most people got dropped off on the outskirts of Nizwa and for most of the trip we had the bus to ourselves! The driver loooked pretty sad that we were his only passengers, as this was obviously not a profitable run for him, but we brightened up his day with a sizable tip in the end.
The mini-bus dropped us off at a Rusayl roundabout outside Muscat. This is a main transportation hub, where a lot of mini-buses end their runs. From there we got a taxi (for a surprisingly reasonable price) to our hotel.