Whether a Japanese verb is transitive or not is a property of that verb, not of its meaning, so the Japanese verb may be transitive when the English equivalent is not. (Often they’re the same, but they don’t have to be.) Consider an alternative English where “I met Tom” was not grammatical and we always said “I met with Tom” – in that world “to meet” would be intransitive. It happens that in Japanese 会う doesn’t use を to mark the person we meet – it’s Xと会う or Xに会う – so it’s not a transitive verb.