In the interest of stirring controversy. I'm going to take the side of Al-Jazeera. Because I'm really not so sure that it's such a bad news organization.
Al-Jazeera is located in Qatar. Qatar being a strong American ally. If there's going to be a best home for the biggest middle-eastern news outlet, Qatar is the best location as far as American interests are concerned.
The only thing substantive that article claims about Al-Jazeera is that they broadcast Al-Qaeda videotapes and the such. How are you going to be a respected news outlet in the middle east and not cover hot stories from Al-Qaeda?
Plus Al-Jazeera is funded by Sheikh Hamad bin Khalifa, the ruler of Qatar (yes I did a little googling and looked at wikipedia before posting). I didn't see it when I checked quickly, but I believe this guy has even made substantial democratic reforms in Qatar.
Here's a book written by a westerner that did some investigating inside Al-Jazeera and made a positive report. He was on NPR's Fresh Air in an interview about the book I heard. I'm sure it's still in their archives if you want to search around on npr.org
Al Jazeera : How Arab TV News Challenges America