I'm not sure that many motor homes have rubber roofs... 5th wheel trailers sure do. A pro is that when properly sealed, they are reliably waterproof, and I suspect they are cheaper to install and to replace. Cons include you have to regularly check/reseal them, they are easily torn and water running off of them can leave black streaks down the side of the trailer.
Welcome to the forum. You have started right by asking questions. Visit different makes and go to all the rv shows. There are several MHs that still have rubber roofs. Coachman comes to mind. Holiday rambler offers the aluminum roof. Winnabago offers fiberglass roofs. Rubber roofs will rip easy but are easy to repair. Probably would be cheaper to replace. Aluminum will dent easy in hail storms and such but may be lighter than others. Easy to maintain. Fiberglass is heavier but should offer better insulation. AJMO
Almost All of your entry level motorhomes have rubber roofs (ie: Fleetwood, Dolphin, Coachmen, ect.). Even some of the mid-range do. Rubber is not a bad way to go. Its easy to clean and seal and easy to repair when damaged(and it will get damaged). A pinecone in 40 mph wind can put a small hole in it. I saw this in Washington state after a bad windstorm on Jan 20 1996. But if you are carefull and check your roof regularly you will be happy with it. Fiberglass roofs crack under the stresses of driving though it takes 4-5 years. they are also easy to clean and seal but harder to repair. Metal roofs are hard to clean before resealing but very durable. However repairs can be a nightmare. Each has its pros and cons so take whats available on the rig you want to buy. The key is to make your choice on the manufacturer by looking at overall construction. Before you buy talking to non dealer affiliated technicians and owners. Me, I recomend you look at Allegro.
It is hardly just the entry level motorhomes that offer an EDPM or rubber roofing. Some others that do, the Cruise Master, Dutch Star, Tropical, Discovery, and many, many others.
The EDPM is the least suseptable to hail damage of the roof materials and it comes with a 12 year guarnatee, if not damaged. Many rubber roofs last far longer than that 12 years and few get damaged in that time, if properly cared for. They are more suseptable to damage from tree limbs, but small green limbs will not harm them. They are by far the most repariable type of roof. There is now a new material that has all of the advantages of EDPM and few of the disadvantages. It is called Brite Tec and comes from the same company, Dicor. It does not chalk like EDPM and is less succeptable to damage from trees, while still light weight and survives hail.