Why is the Tach output on computer fan referenced to the VCC?
The tach output of a fan is open collector which means that it either pulls to ground or allow the line to float. The proper way to read it is to connect a pull-up resistor to high (maximum would be the voltage fed to the fan on the red lead), 4.7K or 10K ohms would be good. This way, when the output is floating, the resistor will pull it high.

If you don't have some kind of pull-up, the line will never get much above zero volts.

I only took a quick look at the instructable, but I'm assuming that they are programming the processor pin to be an input with weak pull-up enabled.

Here's a reference on the fan I/Os: http://www.formfactors.org/developer/specs/REV1_2_Public.pdf