Atmels AtSAM3s gets a bit warm running a test code on my dev board. Is there a problem?
You have some unusually strong pull-up and pull-down resistor choices.

Are R3 and R4 really meant to be 330 ohms?  Also R2 and R13 seem suspect as well.  All 3 of those pins advertise permanent internal pull ups/downs according to the datasheet, making those external components unnecessary.

By adding such low resistances in parallel you are effectively reducing their internal pull ups/downs to something far lower than Atmel intended and are thus sinking and sourcing more current than you probably should be.

Try replacing those resistors with either nothing or something in the 10K-100K ohm range.