I don't think you have to set this up as an either/or – how about you are having valid motherly instincts AND are perhaps a little overprotective?
As wonderful as the special relationship between your son and his last teacher was, it sounds like this new teacher will not provide exactly the same thing. She may not be as warm or patient, she may be determined to give equal treatment to all the students, leaving your son floundering a bit with his expectations and hopes for a repeat of last year. Whether or not she is actually "mean" might be nothing more than comparing poorly to Ms. Warmheart.
There's a wonderful technique taught in How To Talk So Kids Will LIsten, and Listen So Kids Will Talk, in which the parent casually throws out a comment like, "So, you didn't enjoy your time at school very much." Then let the child ponder and say whatever he can say about the situation. This may be tough for your son, but perhaps you could help him complete this thoughts without "leading" him toward your own conclusions.
Kids can reveal the most amazing things, like "I hit Jack before the teacher yelled." Or, "I pretended not to hear when she asked me to sit down." Or whatever.
Even if they were innocent of anything except being themselves, you can then move on to problem solving. Ask the child to help you brainstorm all the ways he might respond to the situation. Write them all down, including some of his ideas. He'll be impressed you take his reasoning so seriously, especially if you have to work with him to figure out what he's saying. Then help him choose a couple of things he can do to make tomorrow's experience better. He'll own the solution, and so he'll try extra hard to make it work.
This technique and many others fill this wonderful little book. It's a goldmine – I strongly hope you'll add it to your parenting library.