Q:

How does this Motor Circuit not ruin the Microcontroller

I came across this instructable about using no external hardware but two pwm pins to control a motor in both directions.  Usually you would use an H bridge.  However, ever since I have had my Arduino I have heard that you are not supposed to connect a pin to another pin.  So how does this circuit works.  It looks like he sends a signal from one pin and in my experience it would fry the board.  So basically, my question is this circuit ok with an Arduino Nano and if so how does it work?  Below is a picture of the setup he gave:

A:

This is a bad idea, but not because two pins seem to be connected directly.  They're not; there is a load (the motor) between the pins, and that motor will take care of different levels between the pins.  High and low will make the motor turn one way, low and high the other way, and the same level on both pins will stop the motor. 
Why is this bad?  An I/O pin can only supply a limited current, and even for a small motor that will peak rather high.  If you run the motor for some time this way you will damage the I/O ports.  An H-bridge, like you mention, is the solution. 
Note that electric motors cause a lot of noise in the power supply, which may cause the microcontroller to reset all the time, so that your program doesn't work. ( The motor may seem to start/stop all the time.)  You need to decouple the power supply with capacitors.