The desert trips from Marrakesh are cheaper as they don't give you the true desert experience. They take you to Zagora, which although is lovely, does not have the biggest or best dunes like those Merzouga. Furthermore, they do not allow you to take in other amazing locations such as the Middle Atlas Mountains on your way there, instead favoring the cheapest quickest route possible which prevents you from seeing the wonders of Morocco.
It takes just 8 hours to get to the desert from Fes, where as getting to the same place (Merzouga) from Marrakesh takes 12 hours! Therefore, it makes sense to start your desert trip off here, in Fes, rather than making the trip to Marrakesh only to realize you haven't cut any time off your journey to the desert!
Starting in Fes, the desert trip cuts through the Middle Atlas where you can visit Berber villages such as Ifrane (known as the "Moroccan Switzerland") and Azrou (a cedar forest where you can see monkeys). Afterwards, our desert experience continues to Marrakesh, taking you through the picturesque High Atlas mountain range.
The desert trips from Marrakesh are cheaper, but don't give you the true desert experience.