We still don't know why Samsung added My Magazine when Flipboard is installed by default on the Galaxy Note 3. By the way, to disable My Magazin on Note 3 completely you need to have Root access, but you have the option to disable opening My Magazine when pressing the Home Button by doing as follows:
1. Open My Magazine.
2. Press Menu Button and then select Settings.
3. Unmark "Open using the Home Key"
Read more Galaxy Note 3 Tips and Tricks