Details, details, it's all about the details :)
Read further down in your guide:
If you have an input that you know regularly goes outside the supply limits then make the series resistor higher. Something like 100R to 200R should be sufficient to keep the current down.
The author recognizes that the diode to +5V is only effective against CONTINUOUS overvoltage if there is not enough current behind it to actually raise the +5V rail. That's why I suggested you leave the 1k resistor in there.
Suppose you apply a 12V source with very low source impedance (like a bench power supply or battery). With no resistor in series and a diode to +5V, then the diode drops you 0.7V and all of a sudden your +5V rail looks like 11.3V!!!
With a 1k series resistor the +12V source supplies at most (12-5)/1000 = 7mA towards the 5V power supply, and the "normal" power source (USB or DC power jack) supplies 7mA less, and everyone is happy.
With a 5.1V zener you can use a lower value resistor (we use 220 ohms on our Ruggeduino) which gives you higher current handling when/if the pin is made an output. If you never make the pin an output, it makes sense to use a higher resistor value.
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