Modern systems have some form of protection against brute force and replay attacks but personally I don't trust them.
I think the main drawback of wireless unlocking is that hacking it is less conspicuous. If you have a device that can unlock a car in 10 times the time it takes with the legitimate key that looks suspicious if you spend that time holding an object to a keyhole, it's completely unnoticeable if you stand a couple meters away on a parking lot doing it wirelessly. Even worse with a method that works on 10% of cars: with a physical keyhole you go from car to car, looking very suspicious, with a wireless device you just stand there and go to the first car that unlocks.
I agree with the inconspicuousness of wireless hacking, but I wouldn't even call it the main drawback: the main drawback is that many insurance companies won't pay a dime if there are no signs of entry at all. Break a window, steal an entertainment system, and the original owner probably gets some money for window repair and a new part. Do the same thing digitally and the insurance company will probably tell you to pound sand.