The reason I can encourage those who seek is that I am not threatened by this. And, I don't think that the God I follow does, either. I believe that this God has gifted humankind with a mind that questions and seeks. This mind is creative and imaginative, just like the One who imagined it.
In response to those who demand explanation or evidence. Sorry, can't help you. And, to be honest, I don't feel that I have to prove a thing. If I am truly to follow Christ, I must, with him, state, “Why does this generation seek for a sign? Truly I say to you, no sign will be given to this generation.”
Truthfully, I don't see any reason to engage the discussions put forth by atheists. I really don't think that discussion is even possible when there appears to be irreconcilable differences. They want proof, all I can offer is experience. Like one blind person in the Gospel narrative I can say, "I know that once I was blind, but now I see." No one can share the blindness I experienced, so they cannot possibly understand what I now see. Please, I hope that no one thinks that because I don't care to debate these issues I don't care for those who would debate. I do. These are people who have meaning and worth. Their opinions are important, but they are only opinions. I cannot prove that God is a loving, caring Being who lives outside, yet inside of our physical universe. (Please, don't make me try to say that again.) Nor, can they prove to me that there cannot possibly be any such Being. In the meantime? I suppose we can agree to disagree and get on with life. For some of us, that may be much longer, (shorter?), than we think.