Does every baby that flaps his hands have autism or some other brain problem?

No: Hand flapping could be a passing stage. It does not always indicate autism or brain disorder. It should likely be monitored for a period of time to see if it continues. Also, i would be more concerned if other symptoms were present at the same. For example, speech delay, lack of eye contact, lack of interest in their surroundings. Insistence on nonfunctional routines, etc.