A retina display has to render 4x the pixels of a regular display, so the slowdown isn't too surprising. Same reason why drawing operations were actually faster on the iPhone 3GS than the 4 after the latter came out.

I played with it more and the UI windows seem to make a huge difference, with them all open it drops to around ~25-30fps or so. I probably had only a couple open to get the original 40fps number. With all the windows closed on the air it actually gets right up to 60 fps. I'm leaving everything at the default settings, enabling 'flying mode' and just leaving it flying straight.

I also tried it on my 'mac' desktop with is an i7 920 @ 4.1Ghz with a nvidia 660Ti running OSX, also using chrome and with all windows open it only does ~40-45fps but pegs at 60fps again with them closed.

Resolution probably makes a big difference also, on both machines I have the chrome window 'maximized' but the desktop has 1920 x 1200 monitors vs the air's 1440 x 900 screen. I'm not sure how webgl handles retina resolutions, it's also possible the nvidia gpu isn't kicking in for some reason, assuming your on the 15" rmbp.