Why UART voltage level on ATMEGA64A-AU are different?
Given that the receive pin is driven by something else, the voltage would be whatever the driving circuit drives it to. GSM modules usually run at 3v3 (actually they often run lower) so there is no reason for one to drive to 5 volts.
The ATmega's transmit pin, on the other hand, would drive to its supply voltage (except to the degree to which it droops under load).  Apparently that supply is 5 volts, which means you'll almost certainly need some sort of level translation to safely feed the GSM module.
Given that you provide no information about your setup, not much can be said beyond that.