PMBok from PMI defines a projectized organization as any organizational structure in which the project manager has full authority to assign priorities, apply resources, and direct the work of persons assigned to the project. While functional organization is defined as a hierarchical organization where each employee has one clear superior, and staff are grouped by areas of specialization and managed by a person with expertise in that area.
Which of the two should be used depends heavily on the organization's type activity and also will influence importantly the performance and deliverables.
A project oriented business managed by a functional organization structure will be slow, heavy and not flexible.
A functional oriented business managed by a projectized organization structure will be confusing, over managed and unclear.
Matrix organization is the most usual with its three flavours: weak, balanced and strong, depending on where the project coordination takes place.
In principle, there is none better than other but it is critical that the organization structure matches the business activity.