You make a fair point, and one that even the Obama administration pursued (the "reset"). No one in their right minds, except for a few Cold Warriors WANTS to have a contentious relationship with the Russians. But there's no avoiding that on some very key issues, the US and Russia just do not see eye to eye. Expansion of NATO; Russian designs on becoming a bigger player in the Middle East; Ukraine/Crimea; more expansionist rhetoric that has Baltic nations as well as strong US allies like Norway on edge.
And then there is no doubt that the Russians sought to influence the most recent election, using the same strategy that has worked so well in E. Europe, Ukraine/Crimea. Those are real issues. If Trump ran on a platform of trying to smooth over those differences no one would fault him for it. Again, this is something even Obama tried. But when your administration in waiting is lying about contact you've had with the Russians; you're unwilling to disclose information to rebut allegations that you're financially leveraged with these people; you take no steps to punish a country that involved itself in our elections; defend Putin at every opportunity (even to the point of arguing a moral equivalency between the US/Russia), etc etc - you can't help but assume there is more to the story.