Let's not forget that he has just turned six and that he has a natural time schedule inside him regarding all his learning, whether it's learning how to walk or learning how to do something as amazingly complex as reading. There is no reading level that he should be at as this school year begins. You have been providing him with encouragement and reading enrichment at home (I hope without any pressure to achieve a certain competency) and we hope that he is in a nurturing class where his teacher can adapt her reading teaching methods to his learning style. I certainly would share with her what you have been doing with him at home. Neither of you should apply any pressure on him to "get with the program". Reading is too complex a learning to insist that his brain do something NOW that it will naturally do later.
As to the seemingly controversial, never-ending phonics and whole language reading debate, I believe that creative combining of both methods has always been the way to go and let's face it, in the English language there are many words that you just have to learn by sight reading. Encourage your little guy in all he does in and out of school and perhaps talk with the teacher about not using the phrase "He's not reading." My guess is that he may be sounding out many words, both in and out of school, and only his successful progress should be referred to, not his inability to "do it all" right at this moment.