Optimizing for search engines is essentially a form of manipulation. You manipulate your site to get the search engines to consider it relevant for whatever keyword phrases you are targeting, which in turn helps you achieve top search engine rankings. While search engines like sites that utilize great content, site structure and whatnot, they don’t like blatant manipulation designed to achieve top rankings.
The worst offenders are those that manipulate without trying to create the most relevant experience for the user. Essentially, they want to be #1 without actually having a site worthy of being there.
Maybe I can put it in other terms. Any married guy will tell you that if he wants something bad enough he needs to convince his wife it was her idea. You can take that same approach with search engines. If you make your SEO manipulation obvious then you’re going to get tagged by the engines once they figure out what you did. On the other hand, if you keep it all under the radar, so to speak, then you can get good rankings and the search engine will, metaphorically speaking, think it was it’s idea to put you there, not yours. And chances are, not only will you have “manipulated” your site into a top position, but you probably manipulated the site into actually deserving it.