We are most certainly not alone in the universe. In fact, we live in a universe so crowded with "others" that I find it very amusing that we continue to ask this question.
1) We are not alone as humans. Each person born on earth is alone. He is locked up in a cage of sensory perception and experience. All the people we see about us are merely actors in our special dramatic performance. But, in truth, once we break free of this ego-centric view of the universe, we can connect to others. Every discovery of a soul mate, a friend, an enemy, validates the truth that we are not alone.
2) We are not alone spiritually. God, of course, is omnipresent, which means that He can be in all places at the same time. This means that each of us can have a unique and intimate relationship with God. If ever we are under the impression that God has deserted us, that there is no one "out there," listening to our prayers, then it is because we have withdrawn from Him, and not the other way around.
3) We are not alone as spiritual creations. Mankind, in all its variety of social and cultural permutations has always recognized the spiritual variety of creatures. With us, they share intelligence to a variety of degree, and some impulse of free will. Djinn, angels, demons, devils, imps, elementals, faeries, vampires, and all things that go bump in the night, keep us company whether we like it or not.
4) Extraterrestrial intelligences are almost certainly prevalent in possibly large numbers. Given that the number of habitable planets orbitting a suitable star are fairly common, astronomically speaking, and considering how many galaxies are similar to our own, there is every probability that intelligent life exists elsewhere. And, from a religious point of view, why would God creat so many distant galaxies and leave them devoid of intelligence? But, even if that were true, even if, by some miraculous celestial lottery, we had an intelligent life form residing near us, as far away as 50 or 75 light years away, we should never expect to hear from them.
If they were to exist we would probably not even recognize them as being alive, let alone intelligence. On television, all aliens are like us. The truth is, there is little reason why something alien shouldn't be so alien as to be unrecognizeable. Even should they look exactly like us and speak the Queen's own English, the stellar distances would prevent any communication between the two of us, let alone travel. And even if such travel were possible, why would any other race wish to visit this troubled mote of unremarkable dust?
Perhaps we are still too ego-centric.