Four of us are going to Spain mid-May and are trying to arrange as much transportation as possible beforehand. We will fly into Madrid, go by train to Barcelona where we will stay a few days then back to Madrid. We want to make side trips from Madrid to Toledo and Granada. Trying to arrange travel between Madrid/Toledo/Granada seems to be a problem. We found "Railbookers" online. They book transportation, lodging and/or city tours. Has anyone had any experience with this company?

You can purchase train tickets strictly from the Spanish rail site. http://www.renfe.com/
Instructions on how to do this is given on this website.
http://www.seat61.com/Spain-trains.h..._www.renfe.com
When using your CC make sure it is Verified.
Some trains cannot be booked online either because they are local trains (Cercanías ) or because you are looking too far a head.
For accommodation try looking at http://www.booking.com/
Tours will be listed in the tourism website for each city you wish to visit. Sometimes these can be prebooked others not.

If you are flying home from Spain, consider leaving from Barcelona rather than returning to Madrid. Such multi-city or multi-destination routings can save substantial time and money.

Most people on this board that have trouble booking with Renfe us Petrabax. I'm sure any of the resellers such as Railbookers and Petrabax charge a fee for the service or mark up the tickets a bit (or both).

None of what you wish to do is difficult to arrange yourself and with a good guide book you can tour anywhere at your own pace.
Toledo is a quick and simple train or bus journey from Madrid, but I certainly do not see Granada as a 'side trip' from Madrid, if you mean in the sense of day trip.