A minor pet peeve of mine. See, the purpose of indenting a paragraph in a book is to set it off from the line above it, so that the reader knows a new paragraph is beginning. (Incidentally, this is also why you don't indent the first paragraph in a chapter or article; there's nothing above it to set it apart from.)
In HTML, a paragraph (<P>) tag will create a double line break to accomplish the same thing without indenting. So indenting after a double line break is functionally redundant.
Double line breaks are preferred because they're easier to spot when scanning a page. On the Web, all the double line breaks in the world won't cost the publisher a penny in printing costs. In the print world, however, it can eventually add up to hundreds of pieces of paper per print run. In that case, indenting is more cost-effective.
Besides, it's non-standard. Indenting paragraphs in a Web page just looks... funny, after six years of double line breaks. Where design is concerned, a certain amount of conformity is a Good Thing.
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