There's no "why" or "why not". They're two different tools for different purposes.
Personally I use raw JPG/PNG when I'm loading external files (i.e. downloaded from web) or when the XNB equivalent takes a LOT of memory compared to a PNG (I've had pixel art spritesheets that took 20x in XNB)
Also when prototyping I have my code reading first for JPG/PNG in local folder and going to the Content otherwise. This way I avoid having to manually add all the files I need.
The only real advantage the content pipeline has is that content loading is faster (i.e. when you load a PNG you must parse it and convert to a native texture format, while the content pipeline does this on compile time) and this really shines when targetting low powered devices like most androids. I must say I'm not a big fan of the content pipeline though.
btw, you can also mod the XNB, it's just less convenient than taking Photoshop and editing the PNG file.