The words roots, routes sound the same but have different meanings and spellings. Why do roots, routes sound the same even though they are completely different words?
The answer is simple: roots, routes are homophones of the English language.
Plural form of root.
Plural form of route.
Third-person singular simple present indicative form of route.
Definitions from Wiktionary, Creative Commons Attribution/Share-Alike License and Wordnik.
Homophones (literally "same sound") are usually defined as words that share the same pronunciation, regardless of how they are spelled.