Connecting BeagleBone Black using serial port - voltage
See this page  http://beagleboard.org/Support/FAQ

You need to have a 3.3 V serial adapter.  A voltage divider is ill advised, because you need to maintain low impedance and you don't want to draw that much current on either side.  If you insist on using the 5 V, then an active level shifter is recommended.

It is not surprising that it worked on the Atmega.  Most microcontrollers will have pins that will tolerate 5 V.