I really don't get what the points of checkpoints is other than rather bad fast travel points.
They don't reduce enemies, they are a constant spawn point for enemies when you either take them or fast travel to them.
I have had tanks, helicopters and around 20 infantry on me about 1 minutes after fast traveling a number of times.
They do however stop you from getting attacked all the time when driving through one, when you take them.
On that point, how do you drive through them and not getting attacked?
If you autodrive/drive slow, you get attacked immediately by guards spotting you, driving just a little faster than the autodrive your tires are punctured and then you are attacked.
I know I could just ride through on a horse, but then why have cars in the game at all?
They seems to have been implemented only as a annoyance and not to improve gameplay or anything else.
