I think jtaby made it very clear that he wasn't referring to cases where it covers search results, but that it covers the website's UI. In fact, those were his exact words.
But this isn't a concession. You can say these things, but every one of them is immaterial to point that the find UI, when present, obscures parts of the page, where potentially those parts are functional UI for that page.
If you think that I'd summarize my comment above as, "there's no problem", you've misunderstood.
" The find bar is presented as an overlay in order to prevent page relayout when the bar is shown or hidden. If the text the user is looking for is under the bar, it will scroll the page, or slide out of the way."
http://www.chromium.org/user-experience/find-in-page
There seems to be a consistent, understandable aversion to pop up windows within Chrome. Excepting the Downloads bar, there also seems to be an aversion to shrinking the display area of the screen. Putting the Find in Page UI overlaying the site causes the browser to show more of the page than if it shifted the page down, something that is clearly a high priority for them (see the Status bar for an example).
Every design involves compromise. I think I prefer the way Chrome went on this one.