Unfortunate, assuming 66 miles round trip for about 17,160 mi/yr the 300 would save you $.02/mi or $326.86/yr over the 600. Trivial expense in my opinion and you wouldn't catch me riding a 300cc bike every day on the highway for 66 miles.
The civic is probably costing you about $.02/mi more, not a Mustachian decision. For the tree huggers (I'm not one, but many here seem downright religious about it), it's a terrible environmental choice to drive a vehicle that burns a bunch more fuel and took a lot more toxic chemicals, plastics, and such to manufacture. Depending on climate and lifestyle a car may be more practical though.