I agree... There are other parts like Laureles, Conquistadores and Belen etc... that are very nice and safe. The hotels in these areas reasonable, like for example Inntu Hotel. It is in El Segundo Parque de Laureles and it has an European flair to it. You can pay on average around $60 per night with breakfast included. Best part, you have everything you need all around you. Food Markets, shops, restaurants etc... Even a Burger King across the street if you are so inclined.
I live in MDE 6 months out of the year and have been doing so since 2009. The city has changed for the better during those years and it continues to show progress. Now with the new tunnel going from Rio Negro Airport to the city, the travel time will be cut to 20 minutes instead of 45min. Expansions to the metro system are being planned for the next few years making it easier to get around the city.
This city is not perfect but then again you can say that for any city in the world. If you want find trouble and pay thru the nose for things, you can do it. There are plenty of places in MDE that would gladly accommodate you if that is what you are looking for. But in general, the city is inexpensive, safe and definetly not a 3rd World Hell Hole. As a matter of fact it is considered by some to be the "NEW" capital of Colombia.
I like MDE... it is charming and that is why I live there.