$3000 is defintely too high for a non-luxury 5 year old car with only 40,000 miles on it. The average US driver spends about $1200 or so on maintenance, repairs and tires per year. And the average car would be about 5-6 years old and have about 50,000-60,000 miles on it.
Volkswagens have above average repair costs and break down more frequently than most other cars.
So you have a double whammy problem, and if you have the dealer do the service, a triple whammy.
I had a full size Chevy and at that age and mileage it cost $844 per year to keep running. Our Nissan Sentra cost $250 to maintain for 10,000 miles at that age. Both cars were above average in reliability and inexpensive to fix.
Your costs with this model are not unusual, but a good mechanic and careful maintenance could lower the figure to about $2000 per yaer.
But, If I were in your shoes, I would get rid of this car and buy something wioth a better track record, like a Honda Accord, Mazda 6, Toyota Camry, of Ford Fusion.