I don't know the rules of the canal, but I highly doubt this scenario. The Egyptian gov't basically has a monopoly and can charge anything they want and write any rules they want. Of course, ships are free to circumvent Africa (around the Cape of Good Hope) if they disagree.

More likely: Ships are required by rules to have an Egyptian pilot on-board during the passage, and there is limited legal liability for ordinary operating circumstances. That said, if an Egyptian pilot was found grossly negligent of their duties, then they would be liable. However, in most legal systems, this is an exceptionally high bar. And, I assume if you pass the canal, you subject yourself to the Egyptian court system. (Read about the big cruise ship that ran aground in Italy. That story reads like text book gross negligence!)