For my project I need to connect Arduino Mega to my Raspberry Pi via USB, since the pi is already loaded with four usb peripherals including a wifi dongle and all its GPIO's connected to something. Is it safe to give regulated 5v down the Mega's 5v pin at the same time being plugged in to usb???
Yes, maybe 100mA, that is not enough for many USB devices.
You can use a usb hub on the Raspberry Pi.