Generated files shouldn't be checked into source code control (related: P.SE: Do I check generated code in to source control or not? SO Should I store generated code in source control). The code generated by jaxb certainly falls into this category.
The logic falls much the same reason you don't check in object files into source code control or the final build itself. They are the programatic output of some other process.
The contents of source code control should be enough to do a build from any given point in time. This may include the .xsd as part of the contract you are given for the API (just as one would check in .h files for a library in the C world).
Having generated source in source code control leads to the temptation to tweak it and it becomes something that you can't generate again. Someone else can't take jaxb and generate the same thing.
Generated source also runs up against the DRY principle. The necessary information to build it is in the .xsd and the build step. Adding the class files that are generated is another copy of this information with no added value.
From the two above points, realize that changing the generated source means (while necessary sometimes) means that the source code no longer matches the definition - it doesn't match the .xsd (or if dealing with a grammar, the source doesn't match the language definition anymore). Consider the nightmare when the application is ported from one language to another and you generate the source from the .xsd and the functionality of the generated code doesn't match that of the generated (and tweaked) code.
Sometimes, the generated source can be very large to the point of something prohibitively expensive to put into source code control. Anecdote: Apache Axis once generated a 4 megabyte .java file for me (yes, 4 megabytes of text) - I really didn't want to have that be something sitting in the source tree (most IDEs freaked out about something that massive).
So no, don't check in generated source. You should only have what you need to do a build and the steps to do that build.