I use markdown for basically everything! It's ideal for technical and academic writing. Keeping everything plain text, and human readable, ensures compatibility and portability. The ability to maintain a single source for content, which can easily be exported to any format, is ideal. Divorcing style from content allows for the application of the most appropriate styling in each finished product.
InDesign doesn't support importing markdown directly. I currently work around that by using Pandoc. to convert markdown to ICML (InCopy) and then using Place in an InDesign file. It isn't as painless as I'd like, but it works and I have to keep Pandoc around anyway as it's ideal for easily converting markdown to HTML, ePub, Word, and a variety of other formats.
I'd kill for APub to handle the import directly. The *ideal situation* would be a Place option, so the APub document will update automatically when the markdown file is edited. Otherwise, I'll need APub to support the import of a file type I can export to via Pandoc to preserve my current workflow.