Vin is connected to a voltage regulator. Voltage regulators have a dropout voltage. This means that if you provide 5 V to a 5 V voltage regulator with a 1.2 V dropout then it will only supply 3.8 V to the 5V pin and the microcontroller. That 3.8 V is supplied to the 3.3 V voltage regulator. In the case of the Uno, the 3.3 V regulator has a dropout of 0.3 V so actually it will still be able to supply 3.3 V to the 3V3 pin.
03david7069:
I read that many people connect 5V to VIN
If it's a 3.3 V board, sure. Otherwise those many people don't know what they're doing and will end up having problems later. If you want to power a 5 V board with a 5 V supply, just skip the voltage regulator.