My son is almost 4 and also has hypotonia. We had an MRI done when he was 8 months old because there seemed to be no specific reason for it. It turns out that he has "diminished white matter" making it difficult for motor impulses to be transmitted from the brain to the brain stem. So his motor skills were very delayed. The official diagnosis is "Mild Hypotonic Cerebral Palsy". He had early intervention PT/OT through the school district from about 8 months until he was 3. He sat up about 11 months, and finally crawled about 15 months and walked around 20 months. At almost 4 now, he isn't the most graceful, but he does everything he needs to. He runs and jumps and throws. Compared to other 4 year olds he isn't as active and you can tell a difference in their ability, but it isn't detrimental at all. The neurologist says that he will do everything he is supposed to, but playing sports may be a little difficult as he may not be terribly coordinated. Oh well.
I will say that it helped a lot finding out what was causing the slow development and low tone issues so we didn't have to wonder. He also has an atrial septal defect, or a hole in the upper chamber of his heart that will need to be surgically closed at some point soon, as well as a few other "soft markers" that could be an indication of a "syndrome" of some sort, but after extensive genetic testing, we have been unable to determine any known syndromes. He is very intelligent and happy and interactive so I am not worried that he will continue to have a healthy, normal life.
As long as your neurologist isn't worried and he is making progress and you are getting the therapy he needs, I would relax and just take things as they come and just enjoy him. My son learned all his letters and numbers and had really good fine motor skills because he wasn't so busy running all over creation and we had time and patience to sit and read and play and do more quiet, academic pursuits. Use the time that you have with him sitting relatively still to just enjoy spending time reading and playing together. It is an advantage that many other mom's don't get with their boys!