How does this overvoltage protection work?
It's pretty simple:
The Zener diode voltage is at (or slightly above) the normal Vcc voltage. For example, a 5.6V Zener for a 5V Vcc.
When Vcc is below the Zener voltage, no current flows through the diode, and the 1k resistor keeps the base of T1 low. No current flows through the collector to the emitter of the transistor.
When Vcc is higher than the Zener voltage, current flows through the Zener diode and through the base of T1. This allows current to flow through the collector and out the emitter of the transistor.
The current through the transistor is high enough to cause the fuse to open.
Short version:
Overvoltage causes the transistor to short and blow the fuse.
Having read the article and looked up the RXE025, I see I need to change my description somewhat.
This protection circuit doesn't shut off power to the protected circuit.
When the input voltage exceeds the Zener voltage the transistor conducts.
The RXE025 was chosen because even in a "tripped" condition it will pass enough current that the protected device (an Arduino in the original example) will continue to run.
The RXE025 turns in to a current limiting resistor to limit current through the Zener diode and the transistor.
The result is that Vcc is limited to a little more than the Zener voltage.
The "fuse" doesn't blow in the usual sense, it merely changes to a higher resistance.
Basically it's a power zener diode circuit. The zener begins turning on the BJT when sufficient voltage is across the line. The transistor takes current and the more that the line voltage tries to rise above the zener voltage (plus a Vbe drop of around 1 volt max), the more current is taken by the BJT.
The BD139 can handle currents up to a few amps and that means it can handle a few tens of watts for a short time period before the resettable fuse activates.
Given that the zener is a 1 watt type, the combination of zener diode and BJT can be regarded as making the equivalent of a 10 watt (plus) zener diode. Of course you could just buy a 10 watt zener but this might cost more than a 1 watt zener and a cheap BJT.