My thinking on this has somewhat changed given the direction we've seen undertaken the last few months. I doubt (but do not yet completely discount) the theory that there was a quid pro quo agreement whereby Trump was approached and agreed to go easy on Russia in exchange for their help in the election.
Rather, I think the more likely explanation for all of this is that they had their hooks in him very deep financially. Given his well known financial problems over the years, his prior ties to Russian oligarchs and financing, I think that Trump turned out simply to be the right guy for them in the right place at the right time.
What we are going to find out is that Trump has decades worth of shady dealings with them, and owes them a ton. So when he won the nomination, the Russians pounced on the opportunity both to play games with our electoral system, and also to take a shot at Trump winning, knowing that if he did he would have to play ball with them.
Trump knows full well that there won't be any signs of explicit collusion and communication of such in the campaign. But he also knows that a thorough examination of his finances will reveal that the Russians literally own him lock, stock, and barrel.