Oddly enough, I've never been particularly comfortable with this verse, as benign as it appears. Whenever I have heard it I have wondered, What about when I am alone? It may seen naive or nitpicky to think that but really, is Jesus saying here that he is only present with us when we are in community?
Considering it though, I find my comfort in the word, "with." When I consider my relationship with Jesus, I don't think of him being "with" me so much as "in" me. We may say things like, "He walks with us," but when it comes right down to it I carry Jesus in my heart -- he's not sitting in the chair over there or something. He abides in me, not in the next room. So perhaps that's all there is to it -- Christ is "in" me, and yet when I am with other believers, he is "with" us.
I've read that the Mishnah, a set of ancient rabbinic teachings and expositions, tells us that, "If two sit together and there are words of the Torah between them, the Shekhinah [the presence of God] rests between them." Jesus obviously knew this saying from the oral traditions that eventually made up the Mishnah, and here gives it new meaning and a new dynamic by essentially proclaiming himself to be that presence of God. Seen in that way, we realize that this simple sentence would have been earth-shaking to his original audience.
One concrete example of this concept comes to mind immediately, and that comes from the Prophet Daniel. In Chapter Three of Daniel, we are told about how members of the court basically tricked King Nebuchadnezzar into having three talented young Hebrew men executed -- Shadrach, Meshach, and Abednego. They were thrown into a blazing furnace despite absolute innocence, but they placed their trust in God, saying:
“King Nebuchadnezzar, we do not need to defend ourselves before you in this matter. If we are thrown into the blazing furnace, the God we serve is able to deliver us from it, and he will deliver us from Your Majesty’s hand. But even if he does not, we want you to know, Your Majesty, that we will not serve your gods or worship the image of gold you have set up.”Once they were in the fire the king was amazed to see, not only that they did not burn, but that a fourth person was in the midst of the furnace with them. Convinced that an angel, a god -- or The God -- was in the furnace protecting the three young men, Nebuchadnezzar had the men brought out and he praised the God of Israel.
In much more mundane situations we can have the confidence of knowing that when we are together in God's name, Jesus is indeed there amongst us, protecting us and guiding us. He is as present with us as he was with his disciples two millennia ago. If we don't hear his voice or see his face, that is not his fault, but our own.