There is an interesting article in the Nation on The New Face of Al Jazeera by Kristen Gillespie. Gillespie writes:
When Al Jazeera was first launched in 1996, it offered the kind of freewheeling, uncensored debate never publicly seen on Arab televisions, and Arabic speakers couldn't get enough of it. The talk shows brought in guests from across the political spectrum, and the channel featured smartly produced news bulletins and correspondents stationed seemingly everywhere. But 9-11 brought a new anti-imperialist and, many argue, a pro-Sunni Islamist bent to the network. (The observations and reporting in this article apply only to Arabic-language Jazeera; in November 2006 the network opened an English-language counterpart, now called Al Jazeera English, which gives no evidence of sectarian tendencies.)Also, there has been a purge of more secular people at the station:
After the March 2003 US invasion of Iraq, Al Jazeera replaced its longtime secular bureau chief in Baghdad, Faisal Yasiri, with Wadah Khanfar, who had reported from Afghanistan after the American invasion in 2001 and then Kurdish-controlled territory as the war with Iraq was launched in 2003. Shortly thereafter, the secular head of Al Jazeera, Mohammed Jassem Ali, was ousted and replaced by Khanfar, whom more than a dozen current and former employees of the station interviewed for this article characterize as an Islamist.It's worth reading the whole article.