Edit: Java is not a language to use for large scale 3D games. Attempting to render complex 3D shapes with texture mapping and lighting can bring your game to a screeching halt.
(( Java is a perfectly fine language to use for 2D MMOs, and non graphic intensive 3D games ))
Eh, I wouldn't worry too much about "rendering complex 3D shapes and texture mapping and lighting", and so on as that's going to be hardware accelerated. It's not like your choice of language is going to greatly impact that.
The biggest pain point in my opinion is the lack of structs in Java. All your math "objects" are exactly that, objects allocated on the heap. So you're going to have to worry about allocations during updating/rendering (gotta be smart about it, e.g. extensive use of pooling). Then of course concerns about performance with a managed language where code is being JIT'ed on the fly. Certainly not going to get the performance of native in that regard, but that doesn't mean you can't do serious graphics programming. Far from it!
If you want a more comprehensive package, jMonkeyEngine is a good platform. I used to use it back in the day, but they've made some big strides the last time I used it (or used Java...heh I'm mainly a .NET developer and personally prefer using C# over Java and Direct3D over OpenGL, but that's me). It has a lot of stuff out of the box, so you may not be finding yourself right from the get go doing complex low-level stuff (or writing shaders).
But if you really want to learn graphics programming I would go with the low-level wrappers around OpenGL or Direct3D (although, are there any D3D wrappers out there for Java?) such as LWJGL. And like Glass said, search for "Modern OpenGL", e.g. programmable pipeline.... --> OpenGL Bible 6th Edition. There's a plethora of tutorials and material out there that use fixed function, which at this point is legacy, so it can be confusing and overwhelming when first starting.