The three phrases have different meanings, so much depends on what you want to say:
Our course will help you ...
If you choose to do X, our course will assist you in achieving X
Our course will let you ...
If you have trouble doing X, our course will help you overcome this trouble.
Our course will make you
Whether or not you have strong feelings about X, our course will push you to achieve X.
Context is important to decide which to use. For example, a self-help speaker might say:
My course will make you a master at getting what you want!
The speaker knows that his audience wants this, but they also respond well to "forceful", aggressive statements. On the other hand, "let you", and "help you" are gentle and non-threatening, and may be appropriate for people who would otherwise resist being told what to do:
If you have a drinking problem, our course will help you / let you regain control of your life.
[Edit] The question has been edited, but these answers should still apply