In most cases, an organizational structure is not chosen, it is imposed. In the case of old companies, the organizational structure is imposed (usually) as functional. As for new companies, the choice of the organizational structure depends mainly on the person in charge of creating the organizational hierarchy in the beginning. Now if the person is objective, he will choose the organizational structure based on:
- The types of projects (as you stated): If there are lots of projects where the requirements are fluid, then it's better to go for a projectized organizational structure. If most of the projects undertaken are traditional, then it is in the company's best interests to go with a functional organizational structure.
- The size of the company: Larger companies are probably better served with a functional/hierarchical organizational structure.
- Thee type of the business: Traditional businesses, such as construction/manufacturing/etc... flourish when using a functional or functional matrix organizational structure. Web development companies thrive in a projectized environment...