There is no difference in the meaning between these two. For, in order to “Agree”, it is necessary to do it “With” another. Therefore, the only difference is in the usage.
When we use “Agree With”, there needs to be a pronoun or object (usually a person… unless you happen to be in Wonderland) directly after it in the sentence.
The statement “I agree.” as a two-word sentence which stands on its own, is also classified as an Interjection. The person does not need to say “I agree with you” because the person being spoken to, already comprehends that he (or she) is the one being spoken to.
And that’s that! Pretty simple huh?
Have An Excellent Day!