As the Suez Canal is owned and operated by Egypt, all charges are paid to the Egyptian government. And yes, indeed, they do charge you to travel on their almost 100 mile long canal. How much you ultimately have to pay for the trip can be a matter of debate, although, in general, one is charged according to the volume of the craft. It is best for a boat or ship owner to completely familiarize him or herself with all charges involve in the trip, as bribes and irregularities have been know to be encountered by the unprepared.
By the way, the canal may be offering discounts this year because business is reported to be off: in 2009, the canal brought in 4.28 billion dollars as compared to 5.38 billion dollars in 2008. The world economic crisis has taken its own toll :-)