Have you checked your folder structure? It seems to me like Express can't find your root directory, which should be a a folder named "site" right under your default directory. Here is how it should look like, according to the tutorial:
node_modules/
.bin/
express/
mongoose/
path/
site/
css/
img/
js/
index.html
package.json
For example on my machine, I started getting the same error as you when I renamed my "site" folder as something else. So I would suggest you check that you have the index.html page inside a "site" folder that sits on the same path as your server.js file.
Hope that helps!