I find my preference depends on the type size and line length. Small type and short lines are better set left aligned. The ragged edge makes it easier to keep track of where you are.
I'm a bit undecided on which I prefer for ebook reading. I've currently got my reader set to left aligned and auto hyphenate off, as I find excessive hyphenation distracting. If I could switch that off without then being subjected to massive gaps in the text I'd probably keep ebooks justified.