This picture shows that many do in fact bike to work and represents only a portion of the bike racks that are scattered all around the garage as well as outside for visitors, both in the public garage and a special covered area. In addition are the many employees who utilize the free access to TriMet and the Portland Streetcar that all regular employees get. Also, it is my understanding that employees do in fact have to pay to park cars, and that the public garage serves all of Lloyd District (for example, there's many spaces assigned to the Land Rover dealership across the street). Lastly, I believe the parking areas predate Metro's use of the site and are from when a Sears store was here.
It is true that Metro does have many fleet vehicles that employees use. While some tasks could potentially (and may) be done using other modes, there is much work that Metro does that is not feasible to travel to on transit (or by bike). For example, many meetings can require a large amount of supplies or bulky items like easels. Some are far away or where high-quality service hasn't been developed yet, and even if taking transit was technically possible, the amount of extra employee hours it would take would not justify the saved fuel, vehicle wear/tear, traffic congestion and pollution. On the positive side, many vehicles are hybrids or fully electric, and pool bikes are available.
Vehicles are also needed for the RID (Regional Illegal Dumping) Patrol, which goes around and cleans up dump sites and abandoned items.
Moreover, Metro manages many parks, natural areas, pioneer cemeteries, the zoo, convention center, expo center, preforming arts venues and waste transfer stations, some of which are inaccessible by transit since plants, animals and the interred don't generate ridership. Besides some being far away, these places can all require tools, equipment and supplies that could not be brought onto transit vehicles.