Problem powering a toy car engine with Arduino Mega 2560

Yes the 5V pin will supply much more current than a digital pin. Your toy car motor will draw far more current than an arduino digital pin will supply. I don't know how you are measuring current but the figures are a long way from what a typical motor will draw. I have a tiny vibrator motor from a mobile phone ( physically smaller the the nail on your pinky ) it draws more current than an arduino pin can supply (around 60 mA). A toy car motor will use at least several hundred mA and possibly more than that. Typically you'll use a transistor to drive a small motor from an arduino pin