I have followed the ifoedit guides many times; enough that I know it by heart. Every time I use this guide I end up with a disc that contains only the movie and nothing more. I would like to know if that is the intention of the guide or if I am doing some common mistake which excludes the menu from the final product.

There are many guides, including one for no menu. Which one are you following?

I am using the first guide called "Basic Guide" under Ifo Edit guides.

I'd guess you're taking step 3 too far. In that step you must make choices as to what menues to keep.