programming Uno with PL2303

I have an arduino Uno board and PL2303 USB-TTL converter. With this converter I could upload codes to the Uno and run it without problems. This is just like the following video.

But I wonder if this method would fry my arduino. In google some people said that you can burn your arduino by supplying power through the 5V pin and people would be expected to use Vin pin for external power supply. But is this true? Could anyone please explain why the external power supply on 5V pin is dangerous?

It is not recommended. The Arduino Uno has a protection fuse between the USB connector and the 5V. When the USB 5V is directly connected, there is no protection.

When 5V is applied to the 5V pin, the voltage regulator (5V voltage regulator on Arduino Uno board) might break. It happened, so that is a real risk.
It can also go wrong when things are connected to the Arduino pins (that can push current into the Arduino board), or when batteries or power to power jack is applied.
Just a bare Arduino Uno with those 4 pins will probably be okay.

I do apply 5V to the 5V pin, but I have added a diode and I know the risks. This is what I wrote about it a few minutes ago : http://forum.arduino.cc/index.php?topic=333711.msg2302750#msg2302750

I would not use such a usb-serial converter. Use one with the DTR signal, to be able to upload a sketch easy.