As often happens, some early bad experiences can make one overly cautious (possibly beyond reason). I'm thinking here of several publishing clients who continued to forbid use of any TrueType fonts in their books—years and years after all issues with some RIPs not properly rendering them were resolved. In the case of exporting PDFs directly from InDesign, I have two tales from the trenches that put me off using it.
Case #1: In of the first projects I designed InDesign CS2, I was playing with all the cool new transparency blending effects (Difference, Exclusion, etc). I noticed that when I used Export to PDF from InDesign, not all of these rendered properly. If I printed to .ps and distilled a PDF, they were fine.
Case #2: Some years back I received instructions from a publisher not to use Export to create PDFs, because they'd found that such PDFs where not fully accessible to reading software for their visually impaired clients, whereas distilled PDFs were OK.
Perhaps in the current version of InDesign, all these issues have been resolved, so sticking with the more time-consuming distilling workflow is no longer justified. Virtually ALL the work I do is for print, though, so I don't mind losing all the layering and interactivity. Besides, distilling an 840-page textbook just took me less time than writing this e-mail.