I've been reading Semantic Web Programming and we used Protégé early on but then in the later chapter on real life Ontologies, we looked at Semantic Web Frameworks and Protégé was not included. Sorry for my ignorance but I thought that was what the tool does... create triple stores, run queries, create ontologies. Can someone recommend some good tutorials or training on Protégé. I found one on the site but it doesn't go far after creating the Pizza ontology.
And how does Jena fit into this puzzle. Lastly, how is RDFa used? I know what it is but can any tool read in RDFa and work with it like a triple-store and ontology? Or is it required to use GRDDL to transform the RDFa? I know that Drupal 7 is giving us RDFa out of the box but I'd like to get a better feel for how this can be used.
You hit on a number of areas in your question, so it's not going to be possible to give you a complete rundown on several very complex topics.
Protege is primarily a modeling tool. You can use it to develop ontologies and schemas, but you're going to need other libraries and tools to build real-world applications. There are dozens if not hundreds of tools to choose from for nearly every programming language and platform.
If you're starting completely from scratch, I suggest you check out these two books:
Semantic Web Programming by John Hebeler, Matthew Fisher, Ryan Blace and Andrew Perez-Lopez. Semantic Web for the Working Ontologist by Dean Allemang and James Hendler
The first spends a lot of time with Jena so that might be a good place to start if you're comfortable with Java development.
If you still have questions, I suggest that you break that up into individual questions that have a chance of being answered succinctly.