Al Jazeera takes an anti-Israel line because to do otherwise would get them ignored. Most Arabs alive today, grew up with mass media that was, and still is, stridently anti-Israel. You've also got to be careful with religious issues. Religious leaders have always had a lot of clout in the Arab world, and they will use it against al Jazeera if the station appears to be getting out of line on religious issues. While al Qaeda and its Islamic radical beliefs appear extreme to Westerners, to most Arabs, they are just considered 'more religious and militant.'
What al Jazeera has tried to do is become the 'CNN of Arabia.' That is, a purveyor of news in a more fair and balanced way than most Arabs are used to. Several other Arab language satellite news networks have become available, but none are as 'free and fair' as al Jazeera. Some of these competitors put up Arab equivalents of the trashiest Western fare (sex and over-the-top talk shows). Others, which are more subservient to the governments that own them, try to give the usual party line using the flash of modern TV production values.
So if you are a Westerner, al Jazeera is not your friend, but it's not your enemy either. Mainly, al Jazeera is trying to get Arab news reporting out of the 19th century, and into the late 20th century.
Al Jazeera, the first Arab language satellite news station to achieve wide acceptance, often gets labeled 'pro-terrorist.' In fact. Al Jazeera is considered, by many Islamic radicals, as a front for some Israeli Information War operation. That's because, while al Jazeera appears overly friendly to Islamic conservatives and radicals, it is actually being quite even handed by the standards of Arab media. What Westerners miss is the fact that Arab language media is normally extremely shrill and partisan. Everything is black (infidels) and white (Moslems), with no shades of gray. Al Jazeera admits that gray exists in the world, and Islamic radicals consider this equivalent to siding with the enemy. For example, al Jazeera interviews Israelis and pro-American Arabs. Westerners see this as normal in the media, an attempt to present balance. But in Arab media, it is considered a waste of time to present a case for the other side. The other side is wrong and evil, and everyone knows that. Most Arab media is partisan, usually owned and controlled by the government, or some wealthy party or individual. Al Jazeera, for example, is owned by the ruler of Qatar, and other members of the Qatari royal family. Despite that, al Jazeera is given, by Arab standards, an enormous amount of freedom. But, on occasion, the royal paymaster will intervene.