There are two components to speak of when discussing how the new facebook profile will effect advertising. First, let's look at the ads put out by facebook themselves throughout the site. Secondly, we'll try and see if the facebook profile redesign will affect applications and the ads which may appear on these apps.
Let's talk about the facebook ads themselves first - These ads will now be appearing in the right hand column but beginning higher up on the page. In the current version, the ads appear in the left column but underneath the applications. This is a better placement for facebook ads as it seems to be more prominent. Have a look at the screenshot below. The blank white space on the right is where the ads will go. Although this is not confirmed, this is the feeling I got while speaking to Rebecca Sawyer of Facebook's Monetization Team at the
Facebook developer garage in Toronto. Note also that the left hand column for ads is 150px wide in the current design and it seems that the right hand column in the new design has room for an extra 15px of width - this could give the standard 120x600 banner a little more white space to stand out.

Now on to custom facebook applications and ads that may appear on the new application canvas pages. Let me first mention that the canvas page will now be 760px instead of 646px - meaning that social networking ad networks should probably be offering a new ad size!
More importantly however than the width change, is how user engagement with applications will change as a result of the redesign. Applications can now have their own tab in the new tabbed profile design - as seen above. Unfortunately however, many apps will end up losing overall user engagement as they are automatically being moved from the main profile page to the new 'boxes' tab.
Really user engagement is what will effect advertising on these applications the most. It seems as if developers who take advantage of the tabs and who have an engaging application will benefit - while those apps that are not that exciting and are not updated will lose daily active users - a key metric in determining how many advertising dollars app developers can attract.
btw, the new facebook profile is still buggy and incomplete but you can try it out by going to
http://www.new.facebook.com. It should be launched to the public next week!