Ummm...
Donald Trump trusts his own intel officers. Obama's, well, that's a different story. Again, he trusts them in most instances. But, the Russia hacking/blackmail thing is a bit harder to believe. For one, the evidence is all classified. So, for all we know, none even exists. And, there would be something to gain from the whole thing. John Brennan once voted Communist, and was appointed by Obama, which would make it safe to say that he supported Hillary Clinton for president over Donald Trump. Hillary fans recently seem to be having trouble admitting that there was a problem with their party, instead handing all the blame over to Russia, who denied doing anything wrong. This, to them, delegitimizes Trump's victory, and allows them to say that their party deserved the victory. Now, if John Brennan is among these people, he would indeed have something to gain from pointing the blame at Russia.
I'm not saying the hacking was completely made up. But, based on those circumstances, would it be unreasonable to deny the CIA's claims?
And furthermore, after being briefed on the matter and probably seeing the CIA's evidence, he seems to have realized that it was likely true that Russia interfered with our elections. But, when all of your facts are the first paragraph of this, I don't think it is that alarming that somebody would trust Russia over Obama's intelligence officers.
Still, if you are alarmed that he didn't blindly accept what intelligence had to say, don't worry. A new CIA Head will soon take power, which will influence all of the CIA (the new director can replace workers if need be, and will play a large part in all intelligence operations). If Trump doesn't trust his own appointee's CIA over Russian government claims, then we've got a problem. But I think that, with his appointee in charge, the CIA will be much less corrupt and much more accurate and truthful - or at least Trump will think it is. Otherwise, well, it would be kind of alarming....