Substituition cipher: The characters in the original message are subbed with some other characters. Example : Caesar Cipher, where the Roman Emperor use it to send message to his general to the field.
It is easy to be broken, 1) the relationship between each characters is not dissipated in the cipher text E[M], the frequency of the characters in the original message is not dissipated in the E[M]. Hence, tools are available to help analyze the E[M] to recover the plaintext M.
Transposition cipher: The original message is broken into blocks. Each characters in the block are "shuffled" in a predetermine order for each of the blocks. The secret key, is the order of the "shuffle". Same arguments as the substitution cipher.