A common phrase used to stress someone's understanding and accepting of a minor disagreement they have with the person they are speaking with. Providing two different pronounciations of the word 'tomato' (the first one with a hard 'a', the second with a soft 'a') represents the knowledge that many things can work in more than one way. The fact that one would probably scoff at person who actually pronounced it the second way is of little importance. Its basically an amiable thing to hear, similar to "hey, lets just agree to disagree" or "to each their own."

It is also one of those rare phrases that lose all meaning completely when typed and read rather than spoken and heard.