Not being able to understand material can be blamed on the previously mentioned difficulties. It can also be caused by a failure to learn good comprehension skills (how to read for meaning). In the worst case scenario, it could be a combination of poor basic reading and comprehension skills. In order to discover exactly what your son's reading problems are, his reading will need to be assessed carefully by a reading teacher or a reading specialist. However, by listening to your son read appropriate material for his age, you will be able to hear how fluently he reads. Then by asking him questions about what he has read, you'll get an idea of how well he understands what he reads.
You can improve your son's comprehension by asking him what he expects to learn before he reads a short passage and then asking him what he has learned after reading the passage. Once he becomes familiar with these questions, he needs to start asking and answering his own questions. Then he will be interacting with what he reads and reading for meaning.