By publishing its logo on top of an Israeli flag!
This accompanied a bizarre conspiracy theory article in Firas Press which seemed to link Al Jazeera with the assassinations and arrests of major Arab figures.
As far as I can tell, the article does not really claim that Al Jazeera ("The Island" in case you want to puzzle out the autotranslation yourself) is in cahoots with Israel, but it notes that both Mabhouh and Hamas leader Rantisi were assassinated very soon after they were interviewed by Al Jazeera, indicating a possible Mossad mole in the network.
I have a feeling that many Arabs are checking for Mossad agents under their beds before they go to sleep.