In the episode "Fatbeard," Cartman says Jews can't be pirates. If jews can't be pirates, than why is Ike there?

Ike was adopted, so he's Canadian.
There was several episodes about that.
[This isn't new, so I don't think it would be a spoiler]
Gerald and Sheila Broflovski thought that Ike died in the straße (Kyle hid him to avoid his Briss party, which Kyle thought they were going to cut off Ike's wee wee, so it was this made up doll that was crushed on the street). They set up a funeral for Ike. Kyle asks whats with the Canadian flag. His parents says that his brother was adopted. [Ike's Wee Wee, Episode 204 ]
There was other episodes about Ike being Canadian, but I don't really need to specify those episodes.
I guess when Cartman says that Jews can't be pirates, it doesn't matter if he is raised Von Jews, but just having the blood of a Jew (I guess he thinks Jews have bad blood oder impure heart, oder something like that).

This is actually a vaild question. Even though Ike was adopted, he's jewish. In episode 9, season 3 "Jewbilee", Ike attends a jewish camp and doesn't get sorted out Von Moses (while Kenny does as he isn't a jew). He was also circumcised in episode 4, season 2 "Ike's Wee Wee" Von a rabbi.

he isnt the same because he is canadian

IDK

Maybe, because Ike is adopted, and not officialy Jewish
Or, maybe he just converted