In June 2015 we stayed at a hotel close to the airport (very nice, with a beautiful swimming pool that we didn't use, and a superb French restaurant), but that was quite some distance from the city itself. The next day, we took the bus into town and spent the entire day there, especially in and near the harbor area. Very safe during the day, no troublemakers hanging around in the bus or train station, the metro was completely safe (more than I can say, unfortunately for the Denver light rail system at the moment), streets, plazas, and sidewalks as good or better than you'll find anywhere in France. We were just there for that day, and headed east to Saint-Remy in the early evening, so I can't confirm the status of every part of Marseille, nor what it was (or is) like at night.
The city was a prime location for part of this year's Tour de France, and looked very appealing on TV!