You just don't want to get peroxide on the roots. Also, it's not a great fungicide/bactericide, purely surface action... if you are going after a disease, you want to choose a product tailored to what you are attacking. I'm not knowledgeable on the fine points here...hopefully Ray will jump in with his store of knowledge.
Roots - especially newly developing ones (the best ones), have tiny hairs, lots of surface area. If those are lost, the root stops growing and may die. Peroxide chews up small bits of tissue (think of how it fizzes if you apply it to a jagged cut) - like those little hairs. So... really damaging to the micro-structure of roots.