I think the problem is that these particular Republican’s mindset is that if someone is on “your side”, they must remain on your side no matter what, and never, never, never criticize anyone on “your side”.
They have seen Stewart mocking Republicans (“their guys”), therefore when he takes aim at something stupid that a Democrat does, it renders them confused.
These particular kind of Republicans are wholly, completely partisan, and they assume that everyone on “the other side” particularly someone like Stewart must be the same. It is puzzling to them that someone can judge situations individually, and not just take a completely partisan approach.