Employers often require it for a variety of reasons (see What reason does an employer have to mandate all travel booking be via the same travel agency? on The Workplace). Some advantages for the traveller include:
- If something goes wrong, it may be up for the travel agent to solve (depends on what goes wrong and why, of course).
- Travel agent will bill employer directly, so that employee does not need to claim potentially large out-of-pocket expenses back later.