There are two big factors at play here: scale and throughput.
First, automation is very good at repetitive tasks. The Wolfsburg plant produces over 800,000 cars per year. It's taken 25 years to make almost 600 Typhoons. That means yearly production is different by four orders of magnitude. It's a lot easier to justify the cost of buying, installing, and programming a robot to save a human from doing the task 800,000 times in a year than just 25 times. This also means that a robot can completely replace a person with a job at one place on the assembly line doing only a few tasks over and over. On the Typhoon line, even if a person only works one line position, they may have many more tasks all over the airplane.
The scale of the Typhoon is also different. It's easy for a few standard industrial robots to access an entire car chassis. It's much harder to access everything on a fighter jet. Larger robots will be even more expensive. Mobile robots are much harder to use with high accuracy. And where you might be able to have multiple humans doing various tasks in the same area, the whole area would have to be blocked off for safety to allow maybe a couple robots to work there.
There is also the factor of processes. A lot of the assembly work on cars is done with welding, which is fairly simple for a robot to do. The Typhoon is mostly assembled with nuts and bolts, which is a much more complex process for a robot to accomplish.
If you break things down to the component level, the balance changes. Drilling thousands of holes in the various components is often done with robotics and some smaller assembly work can be done as well. It's where all of that is assembled into a large structure that humans become the cheaper option.
This also feeds back into the design process. Cars are designed from the start to be easily assembled robotically, because it's much cheaper that way. Not having to design all assembly processes around robot access allows aircraft designers to make things smaller and lighter, a much larger factor for airplanes than cars.