If you are a hobbyist, and you don't want to buy a programmer and you want to save the trouble of configuring and learning to use the programmer... The bootloader is a beautiful thing!!!!.
I've used some other microcontrollers & microprocessors in the past, and I was amazed that I could install the IDE and get the "Blink LED" example running in 5 minutes! With a lot of other platforms, that process could have taken a whole day.
With the Aruino being it's own self-programmer and is it's own development board, and you've saved a ton of time and money compared to starting from scratch.
I mostly agree. Having a bootloader on a arduino development board is very convenient and overall the best way to upload sketches via the IDE. However using an ISP programmer to work with AVR chips you build into standalone projects is often the simplest way to go. And now that an arduino board can be used as a hardware programmer there is no financial choice to make, use either method best suited to what you are doing at the moment in your project(s).