Like saying there is carbon in a water molecule, this is simply not correct. com, net, and org domains all get the exact match bonus in the US, and orgs are not noticeably weaker than coms given equivalent link equity.
A .com with 0 link building will almost always start off on page 1 or 2. Even for a competitive keyword, at worst you are looking at page 3.
A .net or .org will usually start off on page 40.
After 2-3 weeks of link building, with a .com you are looking at a top 3 position. With a .org, after 2-3 weeks of link building you'll be lucky to climb up to page 2.
A .com will always be king, it's the most valuable domain name for a reason.
http://www.google.com/search?q=travel+blog
Now find travelblog.org on that page.
Go search for travelblog on google.co.uk, and it's in the top 3 position.
And sure travelblog.org is #1 there too, but the .org is a PR6 website, while the .com is a PR4 website. That's orders of magnitude higher.
The fact that a .com often ranks higher than its .org equivalent has nothing to do with it being a .com, but rather that its owners have done a better job of building it into a relevant site. You're seeing correlation, but not causation. As you correctly observe, PageRank and other SEO factors are the important thing.
Here are a few more examples of the same principle in action:
http://www.google.com/search?q=wikipedia http://www.google.com/search?q=slashdot http://www.google.com/search?q=php
Same SEO methods on a .com and .net, will always have .com beating out the .net.
All those examples you give, there is no competition, those are BRANDS that choose to reside on a .net/.org domains, there is no wikipedia.com trying to outrank the .org.
We are not talking about brands here. We are talking about keyword centric domains that are targeting keywords people actually search for. So to give you an example, you should be trying to find a bluewidgets.org that outranks a bluewidgets.com, where bluewidgets.org has the same or lower page rank.
Simple experiment, buy these three domains:
hgjhsushrdksjhfkshfkshf.com hgjhsushrdksjhfkshfkshf.org hgjhsushrdksjhfkshfkshf.net
Link them on a single page somewhere, wait Google to index it, and search for "hgjhsushrdksjhfkshfkshf". What tld will Google show first?
But if the .org or .net have a couple good links from somewhere else, they will rank higher. So, you're right on your pure domain keyword ranking, but I am from the opinion that it doesn't matter if you're going to use additional SEO techniques.
.com .net .org worked equally well in getting ranked for the keywords in that domain.
A lot more people buy .com domains. So we see a lot more .com rankings higher up in the search engines.
But as far as my personal tests and experiences show, keyword.org will work as well as keyword.com in getting ranked if the same amount of link building is done for both of them.
The only downside of a .org is - if you plan to sell the site or the domain, a .org gets a lower price than a .com. But from search engine point of view, both work equally well.