Jamie Todd Rubin talks about his love for Obsidian, but not wanting to put his journal in it.
I'm totally in the same boat. I love Craft (and Obsidian before it) for the power of linking, but I love my notebook/journal for writing in. I love the experience of venting a bit on paper, so I can not vent in person.
There is also something about seeing a shelf full of notebooks you filled by hand.