Dealing with CHM files on the iPad and other tablet computers (short-term and long-term)

I've been conversing with medical students -- some of the early adapters for using the iPad for reading textbooks. PDF files work well: tools like GoodReader allow for organization and annotation of texts and iAnnotate allows indexing of your entire PDF library.

CHM files don't play nearly as well on the iPad. While specialty viewers are available, they don't integrate well with a PDF library. Utilities exist for converting CHM files to PDF, but they often fail to paginate the CHM file correctly and also fail to image the mathematical and other technical symbols correctly.

According to the CHM Wikipedia article, Microsoft has dropped any further development with CHM.

CHM appears to be a poor choice for e-books. Why are publishers using it? Do they realize that CHM works poorly with tablet computers? Is there any way to encourage them to stop using this format?