Chem is hard no matter what. I am pretty sure I'm failing my Chemistry course right now.
Never mind, I have a 79.
The only advice I can give you is make sure he gets help. Teachers, tutors, even fellow classmates. A friend of mine who is currently studying Biomedical Engineering helped me throughout high school and saved me from failing on more than one occasion. I still ask her for help even now if I flat out don't understand something.
As for Trig, that stuff can be pretty hard as well...what exactly isn't he getting?
By the way, from my experience, do not take him out of Honors unless you're out of options. Schools understand that Honors courses are much more difficult than regular courses and will take that into consideration.