It’s his baby, after all. In 1994 Jerry Yang (together with David Filo) birthed an Internet web site named after him - “Jerry’s Guide to the World Wide Web” – and since then they’ve been inseparable. While at the age of one “Jerry’s Guide” was more formally christened – Yahoo! Inc. – the relationship between parent and child has remained close. Very close.

Sure, Jerry’s stepped back now and then, knowing his kid needed some space. For years he didn’t even try completely to control Yahoo, content more or less to serve as strategic advisor, while others, Tim Koogle and then Terry Semel, formally filled the post of chief executive. But never once did Jerry let Yahoo out of his sight. So last year, when Yahoo investors became impatient, angry with Semel for letting Google in particular charge ahead, Terry Semel stepped down and Jerry Yang stepped in. Yang took the title of chief executive, thereby officially as well as unofficially playing the part of father figure.

Jerry Yang has cared deeply about his company – and about those who work there. Years ago, after the dot-com crash, when Yahoo had to make its first significant layoffs, he choked up in front of his employees. And even now, as titular boss, he is as well-liked as he is much admired. But as the events of recent weeks testify, Yang and Yahoo just might be too close for comfort.

With the full backing of his board, Yang decided to reject Microsoft’s offer to buy his baby. He claimed that it was all about price, that Yahoo was worth more than the $33 a share that constituted Microsoft’s final bid. But most who know him best insist that Yang never really did want to sell, never really did want to part with the company with which he has been inextricably entwined since its inception.

Of course time might prove Yang right. Time might prove that Yahoo had other options all along, any one of which might yet be more advantageous. Yahoo has flirted with Google, for example, to explore a limited advertising partnership, and with Time Warner, to consider a merger with AOL’s Internet unit. Moreover it’s not out of the question that Microsoft will be back, with a higher offer in hand.

But the days when CEOs have the power to command and control the conversation are gone. Jerry Yang is already being criticized, and loudly, for what he did do, and for what he did not do. Even before the deal with Microsoft collapsed completely, some shareholders had sued Yahoo for rejecting the initial cash and stock offer, which was worth $44.6 billion, but fell in value with Microsoft’s stock price. And now, after Microsoft’s Steve Ballmer picked up his marbles and went home, and after what is at least in the short term a steep decline in Yahoo’s stock price, many more are up in arms.

“Clearly there’s frustration,” said the manager of one Internet fund, which holds a chunk of Yahoo stock. “I am not even sure if Yahoo cares about its shareholders because they didn’t show much regard for shareholders’ best interests in this process.” Yang, in turn, has already felt the need publicly to defend his decision to fend off Microsoft. He posted a blog, insisting criticism of him and his board was “a lot of nonsense and misinformation.”

Yahoo and Yang are both in precarious positions. The question is whether in order to extricate themselves, to save themselves, they will have to go their separate ways. For it’s not out of the question that the bond that ties them is too tight.