That's a guilt-by-association argument that doesn't really hold water.
In its early days Aljazeera was known for broadcasting dissenting views and was perceived as more objective than state run Middle Eastern media entities. Many of its staff were former BBC. Aljazeer was shut down by the Saudi government because it failed to stick with the party line. It had to relocate to Qatar as a result, where it seems to enjoy more independence.
Sources: Control Room (documentary about Aljazeera); Wikipedia [http://en.wikipedia.org/wiki/Aljazeera]