We went to Belize in Feb 2004. We did not go to any all-inclusives and arranged travel inland by bus. It was no problem but you have to be willing to meet and mix with the locals. We also travelled to Ambergris Cay, Cay Caulker and finally to Tobacco Cay. I recommend Cay Caulker it's a funky little town-very safe and definately not mainstream. Ambergris Cay is more spread-out and not too our liking as it's too large. If you need a larger resort type place this may suit you better though! We finished our holiday at tobacco cay and loved it. It's right on the reef and is only a very small spit of sand with about seven small resorts on it. If you go be sure to bring your own snacks as there is no store but the board at the resorts includes all meals (but maybe no snacks later! We also went inland by bus to San Ignatio and went on a cave tour that was later in national geographic. A side trip to the ruins in Guatamala was taken and is recommended. We stayed at the ruins at one of the two hotels there. It's the way to go as you get to see the ruins after the tourists have gone and lets you take sunrise/set photos of the ruins.
We had no problems getting around or finding a clean, affordable place to stay. Just look around when you arrive for something in your price range. We typically spent $35-$70/day US.
Don't bother to rent a car it's too much $ unless you have a group. Also get out of Belize City ASAP there is nothing there as an attraction. If going by water taxi go to the water taxi depot directly-don't waste your time looking around Belize City.
Hope this helps.
PS We really enjoyed our time there.