According to Alice Wellborn, a dyslexia expert of some note: Many years ago, researchers believed that dyslexia was a visual perceptual problem - that it was based in how a person saw letters and words. Now we know for sure, through brain imaging studies, that dyslexia is a problem in the language system of the brain, not the visual system.
Dyslexia is the result of a significant weakness in the phonological processing system, or how a person's brain understands and can use the sound-based reading "code". A dyslexic reader has difficulty cracking that code.