There are several sources of information about GeoTools data access.
The origional research papers explaining the needs that went into the DataStore api are available on the http://vwfs.refractions.net site.
The uDig project has a nice summary of several of the "bigger picture" APIs as part of their GeoConnection Resources.
The GeoTools site itself has a series of really nice tutorials that have not been maintained. The best are those written by Andrea for a university class.
Although billed as advanced, the most careful method by method introduction can be found here:
Finally the user community has started several effots to understand what is going on:
I cannot find it but Bruce has written a good "primer" of feature modeling that provides a lot of background information that is helpful
in understanding "the point".
Additional Examples can be found here (of mixed quality):
