Don't agree that that H1 tag should be your logo and I don't think this is what Yeost was getting at either.
According to this article on his blog, he suggests that the H1 tag on the homepage should be the "Blog's Name."
http://yoast.com/blog-headings-structure/
Single posts then have an H1 equal to the title of the article, and category pages would have the name of the description/tag.
You've got to be careful not to confuse the semantic structure of the content and the branding.
The function of the logo is to provide your content with a consistent brand across all page types. This isn't specific to the home page.
Besides, there are lots of logos that don't spell out their names of the entities they represent so you might want to have both your logo/ident and then say your company name spelt out in the H1.
You could also argue that the subject matter of the home page is not actually the brand/entity name but the value proposition - the "what's in it for you" and I've seen that used at the H1 heading too...
Just ask yourself what makes things easier for visitors to understand/interpret the content on the page depending on the type of site/organisation etc.
<object id="plugin0" style="position: absolute; z-index: 1000;" width="0" height="0" type="application/x-dgnria"><param name="tabId" value="ff-tab-0"> <param name="counter" value="96"></object>