The power structure of the NFL (the owners) does not want a black eye at this point, even if it means justice for one or two teams at the expense of an another. Their logic is simple... from a utilitarian viewpoint, further discussion of the matter hurts the NFL. Apparently Goodell had convinced owners (of franchises that could have been harmed by Patriots spying) that even if they were eventually redressed by the results of a deeper investigation, it would harm the NFL so much that redressed teams would not come out winners either. Since Walsh (the alleged videotaper) has requested immunity in order to come forward, Goodell up to this point has not offered that because he has no incentive to proceed any further with the inquiry.
That apparently has changed- a deal to get Walsh to talk seems closer. Goodell is certainly getting pressure. As much as he has tried to make this thing go away, he is likely getting threats with other actions if the investigation does not continue. You can tell in his press release how he words everything to demonstrate that the NFL is not acting passively, at least not anymore. At this point he is trying to prove effort as much as anything else.