The letter O?
I'm one of many brothers
O is one of the vowel family
I'm in the air and I'm in the ocean,
O is the symbol for oxygen found in air(O2) and water (H2O). Credit to @GileBrt for mentioning this first in comment.
To the ones like Shakespeare goes my devotion.
Shakespeare used 'O' as an exclamation, as was the case in old English (eg O Mistress mine where are you roaming? O stay and hear, your true love's coming)
I get confused by my seeing,
yet completely different my meaning.
(with credit to @MrDeadSven) could refer to the fact that 0(zero) and the letter O look the same but have completely different meaning.
Sometimes big and sometimes small,
Upper case O, lower case o.
when I protect, you won't see me at all.
When the letter protects another vowel it is not heard.