How to get users to read/view the Help section

Sounds more like you have navigation issues rather than needing them to readthe help section.

If you offer a help and they skip it, the navigation should be intuitive so they do not/cannot miss important information.

Perhaps simplifying the navigation structure would be better than forcing users to read the help section, look at iOS devices they are designed to be used with out needing a handbook this is the simplicity that I strive for.

I'm reading the issue differently--is the help center focused on supplementing the content of the course, or how to use the course itself?

If you want to follow a mobile app trend in help, maybe create "overlays" that sit on top of the app screens and point to functions.  You can put different overlays on different screens so people only see the help that relevant to that screen.  For example, check out these overlays for the mobile image editor, Snapseed:

http://www.bing.com/images/search?q=snapseed+overlay&FORM=HDRSC2

Phil, I know, I've been trying to simplify navigation as much as I can, but clearly I haven't cracked it yet.  Unfortunately, none of the users have been able to give much feedback about WHAT is confusing, or where specifically they get lost.  I'll keep plugging away at it.

Kate, the help center is about how to use the course itself (here's where the tutorials are, here's where you can find a glossary, here's how you can jump between demos, etc.).

Minh-Triet, that's an interesting thought.  I could set up visited/not visited variables to the overlays only show up the first time.  People might be more likely to read the info if it's not all put together at once.  Do you think there's any reason someone would not choose 'resume last session' when opening the center?  That's one concern I already have, that those people are having to skip the Help lightbox twice.  Spreading out the help screens would make that problem worse.

There are certain things I do and don't do depending on my audience.  I have found some of my learners struggle with drag and drop, select multiple, etc.  I try to be very clear in my instructions on each slide they have to do something.  I also use arrows to point at things that they have to do beyond 'next'.  For example, on a lightbox slide, an arrow to point at the x in the upper right corner--I know it's obvious to me but have found learners get 'stuck' and don't know what to do.  On questions, I put in italics what they should do--select all correct answers then submit, etc.  A button isn't always obviously a button to the learners, so I try to use consistent colors on all mandatory buttons (next, etc.) and a complimentary/similar color for non-mandatory buttons that they can click. 

Is the course loaded as a SCORM object?  If so, you could have a variable that fetches the student's lesson status, so that if it's "not attempted" then show the help, else hide the overlay at course start? that would run independent of their bookmark status

No, my company wasn't willing to invest in an LMS, at least for now.  I'm hoping to show the value of the site and argue for funds next year.  So it's not a SCORM object, just hosted on our website.