I'm shocked that you're shocked that I'm shocked. People use tools in lots of different ways
I actually just couldn't find the highlight tool in the PDF annotator when I wrote this. I had found the "draw a line" tool, but of course the line isn't transparent. After I posted this in frustration at the inability to do such a simple annotation thing, I figured out how to highlight, and was actually coming back here to edit my above comment.
I don't have an iPad, and need a tool that's cross-platform, and syncs over many devices. For that, Evernote is one of the best I've seen. Everyone always wants more, don't they.