An alternative to using iMovie's Maps function is to create your own animation. It can be done fairly easily.
- Take a screenshot or download a suitable Map that shows clearly both cities (San Francisco and San Jose) at a reasonable distance apart
- Copy and Paste the Map to the Desktop so that you have the original and an exact duplicate
- Open the duplicate Map in Preview (or any graphics app)
- In Preview, click on Tools > Annotate then select Line from the sub menu
- Using the tool bar items at the top of the Preview window, set the color, line style and thickness
- Draw a line between the two cities
- Save the edited duplicate
The next step is to import both Maps into iMovie. Once in the Project timeline (original followed by the lined copy), using the Crop tool under Adjust (above the Viewer), change the setting to Fit for both stills (they default to Ken Burns). Now insert a wipe transition between them. In your case a Wipe Down transition works best. Adjust the duration of the two stills and the transition to suit.
Now you have an "animated" map showing the route travelled (albeit in a straight line over water)!
This technique can be extended to show changes of direction. Simply draw separate lines on maps and use the appropriate wipe transition. A little experimenting will soon give you the feel for it. In your case you could draw lines along the approximate road route between San Francisco and San Jose, changing direction where necessary. It may sound like a lot of work but really doesn't take long.
John