Guatemala has a terrible reputation for crime but in my opinion this was not evident in Flores. We felt totally safe for the for the duration we were there. Apparently Santa Elena (the neighbouring town) is a bit dodgy though - its the nearest place with an atm and I heard stories of people getting mugged at it.
I went to Flores with a group. Nice town but we heard gun shots at 5am. Just don't go in the streets after 10pm because you will see street gangs and, if you're bad lucked like us, you will hear gun shots.
I think that this sign says it all. This warning about crocs and alligators is posted at Petenchel Lagoon. I saw plenty of the small guys but they tell me that they have seen some up to 3 metres.