There are "ruggedized" version of arduino. I forgot what they put into them, but probably something like TVS diodes and 20 to 100 Ohm series resistors on all I/O pins, but you are not going to get such boards for USD 4.
For ruggedness. I've got a feeling the're getting more fragile with each generation. I started with the PIC16F84, and when switching to the AVR's I got a feeling they were a bit more fragile, and they became a bit more fragile about 10 years later. I guess a die shrink does that to those chips, although I do not see a good reason to keep the last I/O stage and protection circuit the same size transistors as previous generations (That would not be a straight die shrink but need a bit of re-engineering). Because of this, I think you're best off with an older design uC. But you also want software compatibility. I doubt you would be able to get much better then the old ATMEGA's. I also got the impression that PORTC (with the analog inputs) on the Atmega8 and 328 is more easily damaged then the other ports, but I do not have enough data to know this for sure.