Sometimes. While it's true that this is often the case, these sailings have become more popular, especially with bargain hunters, which has driven up the prices. Further, transiting the Panama Canal isn't free, and can cost $80,000-100,000 each way for a cruise ship, depending on size and passenger capacity. For both of these reasons, we can look at NCL and see for example that the per night cost of a Transatlantic sailing ranges from $30-$117 passenger/night. their scheduled Panama Canal crossings range from $40-$128+ passenger/night.
Quick Fact - The most expensive Panama Canal 'toll' was paid by Disney Cruise Lines when the 964 foot long Disney Magic paid $331,200 for the privilege.