I found in my time here in Guatemala that checkpoints are a good thing, as long as you are not hiding anything!!!
There have been a rash of robberies by people on motorcycles in Guatemala City. They find stop lights that have long, long lines of cars and two guys on a motorcycle drive up, one jumps off, taps on the window, asks for you money, cell phone, jewelry and then runs back onto the motorcycle and off they go.
Here motorcyles drive in between cars, on the left or the right and when cars are stopped they drive between them to get to the stop light so when it turns green they are off to the races. Just be careful. Do not show lots of jewelry, do not chat on your phone with the window open and just be alert.
These types of things do not happen in Antigua, Pana or Xela since they are smaller than Guatemala City. Walking around at night in Antigua for example is safe, just do not walk along, especially women. BUT then again that is common anywhere today.