Parent-Teacher confrontation should be handled with care. You CAN make things worse. Life lessons are hard at any age, but you should not want your son to avoid them (better he learn them NOW)! Life isn't fair - repeat after me "life isn't fair". ESPECIALLY in the performing arts. If this is passion for your son (and something he wants to continue to do his entire life) he is going to hit rough patches - he better learn now how to cope with that. Moving up the ranks in the performing arts is NOT for the faint of heart! EVERY performer gets rejected somewhere.
Music programs are competetive by nature. In instrumental music kids are always vying for 'first chair'. In vocal music - for solos or parts in shows. Your son is new to this program. If the new-to-your-son music program is already a solid, award winning program the Director likely has years of experience melding talents into the type/style of group he knows equals success. This does not mean your son can't "break through" it just means he hasn't yet stood out.
Both of them (your son and the Director/Teacher) probably need time to get to know each other (we ARE only 4 weeks into a new school year)! However, into ALL of our lives fall situations that aren't fair: co-worker's who don't pull their weight, people who get away with breaking rules/laws, people who get things we 'deserve', bosses/people who don't like us (for no good reason at all) and the list goes on - the sooner your son finds a healthy way to deal with these life frustrations the better.
Your part is first at home: Spend time reminding your son about his successes in the other program. You mention that he had a great relationship with his previous band teacher. Sometimes people instantly hit it off, sometimes people have to warm up to each other, and sometimes oil and water do not mix. Life is always a crap shoot in that regard. HOWEVER, encourage your son to think back as to how he thinks he gained that previous good relationship or 'favoritism' with his former teacher/director...(did you ever stop to think that some other musician in that former group may have felt the same way about your son in that situation as he feels now in this one)? Encourage your son to do the little things that can give him an edge: PRACTICE (teachers/directors DO respond to someone who obviously puts in the time AFTER class time has ended), ALWAYS come to class prepared, offer to assist in class/after class/after school; try-out for new 'chairs', solos - whatever - at every presented opportunity, etc. If your son is good - he should let his talents speak for themselves, eventually the teacher/director may take notice (or not - life sucks sometimes). The BEST lesson you can teach your son is how to handle the 'rejections' in life without losing sight of his love/passion for his music; his confidence or his drive/desire to get where he wants to be in this life. Teach him NOT to give other people so much power to define him. Help him learn how to find that strength from inside!
Your son should be the one to do the talking with the teacher or with his counselor/Vice Principal if the problem becomes extremely blatant. Your son needs to learn how to confront injustices he sees in his world in a courteous, thoughtful manner.
YOU can make a difference (in the background, mom) by volunteering when things need to get accompished, donating money/goods/time and services. Get to know other parents of group members and listen to their experiences as group veteran's or neophytes. If there is REALLY a BIG problem with this teacher/director they will know it and speak freely of it. Always plan any comments you might make to the teacher/director VERY strategically and NEVER be an in-your-face 'stage mom' unless the situation absolutely warrants it.
Performers have egos (your son's teacher/director may not be immune to that). Your son will have to continue to develop his maybe with this teacher/director's help, maybe in spite of it.
Taking a line from "Chorus Line"...."this man is nothing, this course is nothing, if you want something go find a better class and when you find one you'll be a/an ____________ (she was an actress, but you can substitute anything in this blank) - and I assure you that's what finally came to pass". Find other opportunities for your son to learn and play: community groups, youth bands, honor bands, all-district bands, private lessons. Find other places for your son to excel - sports, other instruments, academics, clubs. The more 'well-rounded' he is, the better adjusted he'll be AND the more successful later on in life. Teach him now to NEVER puts his eggs in one basket.
Finally, keep life in perspective...Middle School is NOT the end of the road - it is only a stepping stone (and truly, in the grand scheme of things...not an all so very important one). Yes, Middle Schoolers make some of the most monumental leaps and decisions of their lives RIGHT NOW, but these Middle School experiences should help mold them, not define them. Help your son learn that life is an on-going teacher. So much else comes into play later in life: maturity level, experience, talent, ability....just because these things may not be recognized in Middle School doesn't mean they don't exist. Nurture them and watch them grow!!!