There are flyable BF-109s* but only a couple, and there are several of the Spanish ones left over from the Battle of Britain movie. They were given after production to the lead pilot, who kept them in a hangar in West Texas.He died a few years ago and they were brought out of retirement for this film. The reason you can't use the real ones is that mixing and matching would look odd.
* They are BF-109s. The term ME-109 was used by the allies frequently, but is wrong. They were designed by Willy Messerschmitt, but the production was done by Bayrische Flugzeugwerke (Bavarian Aircraft Manufacturers), and by German government policy, aircraft were denominated by the manufacturer, not the designer.