The issue of charging for use is a constant debate between photographers, and in many ways it comes down to the kind of work you do and the clients you have. Just "charging for the work you do" (an hourly or daily rate) sounds great in theory, but doesn't always work out well for the photographer in practice.
Let's look at two different assignments and see if that helps.
Assignment #1: A full day event shoot, covering a corporate meeting then a reception and dinner in the evening. The client is a mid-size regional company, and they will use the photos on their web site, and in an internal newsletter, and probably give prints to the attendees from the dinner. The photographer will spend 14 hours shooting, then another day (minimum) processing and delivering the photos.
Assignment #2: A photo of a child in a park for a national ad campaign. The client is a multinational chemical company, and they will use the photo in an ad in Parade Magazine to promote their brand identity. You meet the art director, the model, her mother, and the stylist at a local park and shoot for 20 minutes or so, until you have exactly what you need and the kid is getting tired. You'll spend another hour or two processing and dealing with the art director.
All told, assignment #1 will take at least two full days of your time, and assignment #2 might take a half day total. If you are charging an hourly rate, then of course the event photography will cost the client a lot more -- but the second assignment is *worth* a lot more to the client and the photographer, and should cost a lot more. (A LOT more.) And if the client from #2 comes back later and wants to run the ad in another national magazine, they should and will pay another usage rate for that additional use.
The key is that clients should pay for the use they get out of your photos. This protects BOTH you and the client -- they don't need to pay for usage that they don't want, and yet they do pay for making money from your photography. To use your own work as an example, if you are licensing your photos for the client to use on a web site, the client is paying a lower price for that usage. If you knew from the beginning that they would want a printed brochure as well, you would (I hope) have charged more. Not a lot more, maybe -- but something to indicate that the extra use has value.
That said, there are some markets where the clients simply won't pay for use. Any market where there is a glut of photographers, and/or the work is seen as "easy" (hah!) will end up with fairly low rates. In many places (not sure about your location), the local real estate market is like that -- with the exception of very high end properties. In that case, charging for use probably won't work at all.