I have had this problem for the past 4 years and I have still not found a solution. DS has eczema and cannot wear polyester/acrylic/wool; shops don't sell school cotton trousers in navy. I have tried John Lewis, BHS, Debenhams, Next, Gap, Old Navy, Woolworths, M&S, you name it.
The corduroy trousers from M&S would not be acceptable at my DS school so if yours accept them, great. I have resorted to GAP navy chinos which are 100% cotton but at £12 a pair, they're costing me a fortune as they have to be replaced regularly; the knee area becomes worn out really really quickly (within 6 weeks they look a mess) and my DS doesn't even play sports or do any type of 'rough play'.
This website has navy school trousers which are 100% cotton but they hardly have any sizes, the prices are ridiculous and I don't even know if the product is long lasting: http://www.lint-kids.com/acatalog/Boys_Clothing.html
Some Asda supermarkets do grey cotton school trousers which are great in shape and long lasting. I once bought a pair and dyed them navy; they came out great and lasted a long time. DS didn't react to chemicals from the dye. However, I have never been able to get hold of cotton school trousers in Asda again so I suspect they no longer make them.
It makes me angry that our children are forced to wear polyester and acrylics against their skin when most of us wouldn't choose to wear such fabrics ourselves.