That's something inherited from their comical theatre tradition that made its way into manga where it grew into a very codified system (and if you don't know it, you miss a great deal of the meaning in manga). It's basically a storytelling shortcut that make the emotions of the characters plain to the reader, though there are codes for other things as well (flashbacks show with black border, out of focus frame usually in anime) and quite a few false friends (for instance, the "thought bubbles" in western comics are not thought bubbles at all in manga/anime, it rather means the characters are whispering). The manga code made its way into anime, especially those derived from manga, though it's less prominent there, and even in manga many authors avoid the "system" at all cost (it has a comical connotation to Japanese)

It's not meant to be realistic, most often it's used to relay how the character feel inside, especially when it's shown on backgrounds with animation. It's not happening, it's just in the character's head.

Personally, I'm rather used to that in manga, but I could do without it in anime (though sometimes like in FMA, I found it funny - it really depends on my mood).