Hi Lamiaa,
In my opinion working for in a matrix organization is more difficult for the project manager, due to the fact that cross functional team situation, such as sharing resources and staff. Often times multiple team members are involved in multiple projects with different project managers, thus coordinating meetings and deadlines may be slightly difficult. While in project based organization, the project manager has full oversight for the project, as a result if something were to go wrong in the project, the project manager of the project based organization may have full responsibility.

Chris