Well the answer starts by taking focus away from the book, the nature of writing, style and flow, and focusing on the characters within the plot. The protagonist is therefore the main character or the "hero", though in certain instances this is not limited to one. To help remember this think of "pro" as being for something and good, it helps me!
Before you start writing your book it’s important to spend a while thinking about your protagonist in great detail - what makes them tick? What are the defining traits of their characteristics? How would they react in certain situations? What are their strengths, and equally importantly, their weaknesses? All these are vital to explore in detail before you focus on the plot; without knowing your hero inside out, you run the risk of the reader not understanding them, or worse still, not connecting.
A key point to remember is to make your hero seem real (even if you write fantasy). No-one in real life is perfect, that is one of the joys of life - everyone has their flaws. So spend some timing understanding what your hero can't do or is scared of, allowing the reader to see beneath the tough exterior or the pristine surface they portray. These points can be small; a fear of heights, spiders, swimming etc may not necessarily affect their journey through the story, but give the reader snipetts into their psychy which are invaluable. When writing Salvation this is something for Alex I spent considerable time on. Without spoiling it for those who haven't read it yet, I wanted the reader to see that he was tough as nails, but underneath constantly reminded of his horrors as a child.
A useful tool to ensure continuity in your story, particularly if it's an epic, is to list your protagonist’s traits on paper or a spreadsheet. This way not only can you catalogue their physical profile, but other intangibles such as their mentality in pressure situations, what they love and hate and their emotional state as the story progresses. These things are important as your story develops, ensuring your protagonist stays true to their characteristics throughout.
Often the biggest criticisms aimed at first-time authors is their failure to develop their characters, creating heros who are flat and one dimensional. Deeply understanding your protagonist before you write the plot helps to ensure you don’t fall into that same trap. Dedicate the early chapters of your book to detailing your hero's weaknesses as well as strengths. Hopefully as they progress through the reader will connect with them more, seeing them mature as they overcome the challenges facing them as the book progresses. Remember you want the audience to travel every step of the journey with your character, at times whether they want to or not!
Final point of note for the current vogue of killing of protagonists throughout a story (thanks mainly to 'Game of Thrones' R.R. Martin). For this to work you need to have another one or two background characters ready to step in and lead that the readers will accept going forward. Whilst the shock of a death the reader might not have seen coming will win you short term plaudits, if there is no one left to connect with or to care about, then you will lose the reader.
So in summary spend time getting to know your hero inside out - without them your story is nothing more than words!