Hey fellow transit hackers,
I'm Nick Doiron (@mapmeld), a 2012 Code for America fellow and one of the devs behind Chicago's transit future map at http://vision.transitfuture.org/
Like you, we had a lot of cool visualization stuff which didn't work on mobile. There are also a few places on your site where the text is wider than the viewport, or scrolling laterally jumbles things up. Fortunately, it looks like there are a few lines of HTML and CSS which will get this thing fixed. If only designing transit networks were so easy!
HTML: replace your current viewport tag. Make this thing a fixed-width single column site.
<meta name="viewport" content="width=device-width, initial-scale=1, user-scalable=no">