I wouldn't have an issue with an (understated) ad at the end of an occasional chapter. How would you feel about that... just curious.
Being an author and eBook publisher I must say I'd consider that very annoying. The only two places I'd accept (and consider) ads are before the very first chapter and after "The End". And on a separate, new page. But never ever as part of the text.
Sure, the main problem with ads at the beginning and the end is - aside from maybe being removed by a script - that readers would simply skip those pages, ignore them. They simply wont grab readers' attention.
May change on the iPad with full color and animated GIF dogs (the living nightmare of the '90s web).
Finally, advertisements for other novels of the same author or the product line of the publisher are as old as pulp novels or paperback books. So this should be more than acceptable in eBooks.