Some people believe that Al Jazeera is Anti-Israel, which would make it out of alignment with US foreign policy.
For the record, for the Israeli side, I gather they actually (privately) like the station because it was the first Arab station to interview them. Whenever they report about an Israeli issue, they actually get an Israeli to talk about the Israeli point of view.
The problem is not with Al Jazeera, it is that it is the only station with global reach that actually speaks truth to power, challenging those with power on any side. They alone remember that the journalist's role is to comfort the afflicted and afflict the comfortable.
(The one exception is Qatar, which they never report on, but frankly nobody cares about that.)