Title was changed to be a bit less inflammatory now, or is it flammatory? I think they both mean the same thing...
Native English speakers (as with all languages) learn how to speak years before they learn how to read. This makes inconsistencies in letter sounds irrelevant to having good conversational English and leaves learning the inconsistencies later, where you learn common rules that cover most of the language and absorb all the rule breakers while reading.
One thing he notes was that originally there was no spelling consistency because there was no need due to limited written communication. Then as reading and writing became more widespread there became a need for consistency. This took something like 40 years to complete. Unfortunately half way through that period newspapers and dictionaries came out which resulted in some words being consistent and some not.