Reorder the page so that it is at the same level as your home page. This is what is referred to as an "orphaned page". These pages can be linked to and viewed, however, they do not show up in the same page tree as other pages. Caveat: when you're on the orphaned page, you will not see the primary page tree.
If you have a use case where it's more like you just want to show select pages in your page tree, you can go to space tools > look and feel > sidebar, header, and footer. You can use wikimarkup to build your menu. In this case, you can then hide your page tree and only have your selected menu appear.
Restricting a page will also remove the page from the sidebar for those who are not listed in the restrictions. However, then this page cannot be viewed by those people even when linked directly to it, if that's your goal.
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