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I think a lot of it is because Cowboy Bebop's run on Adult Swim was the first introduction to serious anime for a lot of American fans. The newness of the genre made for a larger impact on viewers at the time, plus nostalgia has a way of screwing with objectivity. It's also a rather audience friendly show that manages to appeals to plenty of people who aren't core anime fans.
Another factor may be that Bebop suffers in many ways compared to more modern fare. Dated animation, resolution, and style are the obvious ones. The "cowboys in space" genre is also quite a bit more crowded now. More importantly though, serious shows have gotten away from the episodic format that dominated when Bebop was made and have settled on a far more serialized format. Casual viewers prefer the episodic format since the show remains comprehensible even with missed episodes. Core viewers prefer more serialized shows as plot arcs that last longer than 20 minutes are more rewarding.