Why do words that sound the same have different spellings?

Why are there so many different spelling rules in English? We have many words that sound the same but have different meanings (homophones). Here are some examples:
-ate, eight
-bare, bear
-cell, sell
-chord, cord
-genes, jeans
-know, no
-thyme, time
-we'd, weed
We have so many spelling options because English is an amalgam of many languages. Another way to describe it is that English has many roots. Welsh, Anglo-Saxon (Germanic), French, Latin, and Greek all have contributed words and their spellings to English. Here are some of their influences:
-C or G making the soft sound (/s/ or /j/) it come from Latin
-CH for /k/, PH for /f/, and Y for /i/ are from Greek
-silent letters such as k in know were added to make them seem French

Orton-Gillingham methods teach these spelling conventions so children who can't remember the way a word looks will be able to spell it by sound.

A fascinating book describing the progression of English from the beginning is The Adventure of English by Melvin Bragg. The content of the book has also been presented in a 5 hour documentary of the same name.

Why is spelling so hard?

Most of us depend on spell check to catch our spelling mistakes when we write. What would we do if we didn't have spell check? Do we memorize every spelling? Do we know certain rules that help us? I'll bet you remember this rule we learned in school - "When two vowels go walking, the first one does the talking." Unfortunately that rule works for less than half of English words with vowel teams.

What do we do when we hear the sound:
ew as in few,
ea as in breath or great,
ow as in cow,
au as in auto,
oi as in oil,
ou as in house,
eigh as in eight?

Often teachers fall back on the statement that these are exceptions to the rule. Actually, they follow a different rule - ones that we just haven't learned yet. People to whom language comes easily, pick up these different spellings, but people who struggle with language processing must learn spelling rules in a conscious way. When they do, they actually learn more completely than others and can tell you why something is spelled the way it is rather than just "feeling" that it looks right.