I think the reason in general is simply that org-mode is better, i.e. more carefully defined. I'll mention the things I like more specifically:
- Link syntax in markdown is something I never remember how it goes. Org-mode is [[link][description]].
- Text styles in org-mode make more sense. In markdown, * is used for italics, * for bold. Additionally, * is for lists, which might be confusing.
- Markdown blocks are freaking awful and seem to work by luck more than anything else. Code blocks even worse -- they are made by indenting 4 spaces or a tab! I couldn't come up with a worse way to do that even if I tried. Org-mode has clear #BEGIN_xxx / #END_xxx blocks.
- Markdown has a weird YAML frontmatter syntax. Org-mode has keywords which can be attached to the whole document and properties, which can be attached to every heading.
- Org-mode has tags.
- Org-mode has timestamps.