You don't mention what you expect in a hotel. As you come into Flores, if you turn left at the very first street you can do so, there are several inexpensive ones you will see along the way on the right. There I stayed at the El Faisan and thought it was fine.
On another occasion, I stayed at La Casona de la Isla, which has a pool and is online. However, it costs around $40 US for a double. I consider it a splurge, but it was worth it for me after 7 days in the Peten Jungle.
The beauty of staying in Flores is being able to experience the almost mystical sundown over Lake Peten Itza. This is best done over dinner with a beer or two, but without anyone who will chatter and ruin it for you. Try the Sunset Cafe or Hotel Peten for this.