I'm learning python (and programming in general) through Runestone Interactive. What do people think of that site as a place for beginners to learn python?

Also, is there any harm in trying to learn perl and web design languages at the same time? I'm concerned about becoming confused.

I don't know Runestone Interactive. About languages, my personal opinion is that you are wasting your time learning perl at the same time as python. Both languages can be used for the same tasks and you will end up not using perl because it is older and harder to use than python. There are many languages to learn. You could learn php to start web development.