There are a lot more details than this, but let me water it down and make it easy for you. From each Disney resort (which means hotel), there is DIRECT transportation to each of the four theme parks, as well as DownTown Disney and the water parks. The form of that direct transportation is USUALLY a bus. So, for example, if you're staying at Caribbean Beach Resort, you walk to a bus stop (there are 7 at CBR, one for each "village" plus one for the food court/pool/shops area). If you stand at that stop for about 15 minutes, there will pass by a bus for Magic Kingdom, a bus for Epcot, a bus for Animal Kingdom, a bus for MGM, a bus for Downtown Disney, and a bus or two for the water parks (I'm not well-versed on the water park details, but the general idea works for the purposes of this example). The buses are very clearly marked on the "digital scoreboards" on the front and sides of each bus. You get on the bus at your resort, you get off at the destination. There's no exact schedule of times, they just run throughout the day. Getting back is just as easy. Outside each park/DTD/water park are clearly-labeled bus waiting areas. You just wait at the bus stop with the sign for your resort.
Grand Floridian, Polynesian and Contemporary are on the monorail. People staying inthose resorts can take the monorail directly to the outside of Magic Kingdom. They can also ride a monorail to something called the Transportation and Ticket Center, which is not as vital and important as it sounds. At the TTC, they can get off the monorail and get onto another monorail to go to Epcot. But if people in those resorts want to get to MGM and Animal Kingdom they wait for a bus at their resort. In addition, people staying at Contemporary are close enough to Magic Kingdom to walk (and it's one of the very few places in WDW where there are sidewalks to make walking along a street safe; Disney really doesn't condone walking ANYWHERE along the streets, except for the above -- they want you to be safe and take their transportation instead).
There are some resorts in the "Boardwalk area" where you can catch a FriendShip boat (or even walk) to Epcot and MGM. People staying at Wilderness Lodge and Fort Wilderness Campground can catch a boat to Magic Kingdom. There's also a boat from one of the Port Orleans resorts to DownTown Disney.
Getting from resort to resort is another story. It can be time-consuming, inconvenient, and definitely not quick. Let's say you're staying at Pop Century but you want to get from there to dinner at Boma, a restaurant in Animal Kingdom Lodge. You'd have to take a bus from Pop to any of the theme parks or DTD, and then from there catch a bus to AKL. I'm not up on my geography, but in this case it would probably make the most sense to take a bus to AK and from there a bus to AKL. I just don't bother with such things, since when we travel with out kids we eat counter service almost all the time, anyway, so we're not going to bother getting to another resort just for a counter service meal.
It seems confusing, but it's not. All you need to know is you can go DIRECTLY from whatever resort you're at to whatever park (or DTD or water park) you want.
You really only need to know the details about the ONE resort you're staying at. And if you get confused and you're not sure of the best way to get from your resort to wherever, there are plenty of CMs to ask, and maybe even a nice fellow guest or two.
