I was unaware that USB was so voltage sensitive. If so, what about the tolerances of the resistors? The design doesn't say what the tolerances are, just the values.
I have seen some designs where instead of using zener diodes, is just runs the ATMega at a lower voltage. However, rather than have some sort of regulator, the designs simply uses the forward bias voltage drops of 2 diodes.
I was thinking about doing that and use an ISP interface to download sketches.