Yes, two 1.5v AA batteries (a total of 3 volts) will safely run a 5v fan with no issues at all... there again, lithium cells are gonna give you longer lasting performance. A 3 to 5 volt rechargeable lithium battery pack may be an even better way to go in the long run.
Also, when purchasing these small fans to put in your helmet... take a look at the rpm rating and cfm the fan puts out. A higher rating can really help with better airflow and performance in heat-related trooping situations.