Making ontology in Protege or by Jena API library in Eclipse(Java coding)

Question 1

It depends on what you actually want to do. Are you trying to build a new ontology from scratch? Do you have an existing ontology that you want to extend by adding some data. Are you generating lots of triples using pre-existing classes and properties, based on some data you're already processing in Java?

Protege offers a GUI that allows you to create the ontology more quickly. It also gives you a graphical overview of the ontology in creation. It's sometimes hard to get the big picture even with all this help. It's a powerful tool for overall ontology authoring. Writing an entire ontology by scribbling Java code line-by line seems a gruelling task to me.

Writing plain Java code to create an onthology would be very difficult and inefficient. On top of the complexity of RDF itself, you'd need to understand the Jena API. IMO, it only makes sense if you have a well-defined ontology and you're really sure what kind of triples you want to add. In such case, using Java code to interface with some data source could save you a lot of time. Provided that you know Java itself to do it efficiently.

In your case, sticking with Protege seems the most reasonable option.

Question 2

The answer is yes: it's perfectly possible to create a no ontology through the Jena API and Java code. The difference between Protege and plain old Java code is the task you need to perform: if you need to inspect an ontology or create a few concepts manually, Protege allows you to do it fairly quickly without writing code first. If you need to execute some repetitive task, on a large number of entities, or carry out something else for which Protege does not cater, then you're better off writing Java code. This is not different from a question like: is it better to use a text editor or write a Perl script to edit text? It very much depends on the exact task at hand. Both are possible.