You're comparing an auto search function with human intelligence. If a publishing company paid money to have a professional indexer index the book, they obviously see value in that index (and yes, could pay extra for it in the ebook, but still - the manual labour in converting one is crazy).
Not all books with indexes would suffer greatly without them, but some surely would - particularly for use in reference/research. The index will point readers to the most useful, relevant topics - rather than an overkill of low relevance search terms.
Regardless, I didn't come here to defend the index, I don't really care enough (although I think we should push for high standards in ebooks, as a print book really is a simple thing, and its electronic counterpart is getting carried away with bells and whistles while dropping off some historically important features that made book design an art and reading a pleasure) - I came to ask if anyone could help the process of creating one - particularly after having found it continually useful in some of the reference ebooks I use.
No dice? Ok. Thanks anyways.