What really bother me about this channel are:
The selective and biased coverage: I really never knew that Qatar was an utopia! And you can not air religious programs on a news channel. Create Al-Jazeera Islamic channel and air as much Islamic programs as you want, but you can not shove Zaghloul El-Naggar's humbug on the scientific miracles of Islam down our ears as if that was real news.
Demagoguery and intolerance is what they promote: While they claim that they promote freedom of speech and other things that sound civilized, they really do the opposite. Programs such as "The Opposite Direction" - I recently learned that its anchor, Faisal al-Qassem, holds a degree in drama, and was a bit disappointed that I could not figure this out on my own - are all about shouting and slandering. I mean where on earth do you find a news channel where people call each other "traitor" while discussing their different opinions and views?
Irresponsible journalism: The channel deliberately mistranslated and added to a scientific paper that was published in 2009. The paper recommended a small change in the twig of hominins in the tree of life, but Al-Jazeera claimed that this paper nullified the theory of natural selection. (I wonder how many times this theory was nullified according to Muslims?) This reckless journalist blasted into smithereens any faint hopes for tolerating this theory in the Islamic world for the coming few decades, and the channel never apologized for this mistake. Not like this is the only scientific or historical mistake they have perpetrated.
The worst sports commentary on Earth: During world cup 2010, I was really shocked by some of the comments I heard by this channel's commentators: lamenting Mussolini's days, calling the whole of South Americans irrational, and labeling Japan as a developing country, to name only a few. Makes you thank "God" for the option of muting in TV sets.
