Many, perhaps most, visitors to Belize do both, if not on the first visit then on the second -- it's called a surf n' turf. Typically, tourists spend some time on one of the cayes, most likely Ambergris, and then some time in Cayo District at a jungle lodge.
Belize is a small country and getting back and forth is fairly easy and quick.
A few hotels have tried setting up reef and rainforest partnership programs, offering packages at a beach resort and a jungle lodge, but in general those parterships haven't lasted too long. There are a lot of reasons, but mainly it is that there are a lot of good jungle lodges and a lot of good beach resorts, and visitors like to make their own decision about which one they choose -- they might like the beach hotel but prefer another jungle lodge, or vice-versa.
Belize books and publications by Lan Sluder:
Belize First Magazine (http://www.belizefirst.com
Fodor's Belize & Guatemala Guide (new 4th edition coming this summer)
Adapter Kit: Belize (the first and only comprehensive guide to living, retiring, working and investing in Belize -- a best-seller on Amazon.com)
San Pedro Cool (the first and only visitor guide to Ambergris Caye)
Belize First Guide to Mainland Belize
UpClose Central America
Belize Book of Lists