Even medium sized sport or sport touring motorcycles (e.g., Honda VFR) aren't cheap to run. The engines are tuned for performance not fuel efficiency and usually need premium fuel, so small cars are about as cheap to re-fuel per mile. Also the maintenance cost that killed me was tires: You have to pay around $500 dollars for (two) good tires on a motorcycle every 10k miles (if you're lucky) whereas I spent only $200 at Costco for (four) tires for my car that should last more than 50k miles.
Also consider than motorcycles depreciate faster than cars and the resale market is less liquid so you lose more money when you sell.
Summary: Buy motorcycles because they're fun, not because they're cheap!
Granted a 50cc scooter would certainly be cheaper to run than a car but then you're restricted to city streets (i.e., no highways).