Israeli intelligence has stated in no uncertain terms that the attacks came from Gaza, and PM Benyamin Netanyahu said that the terrorists who were behind the attack were killed in the retaliatory attack against the Popular Resistance Committees. It seems likely that the IDF shared some of their evidence with Israeli reporters off the record, as a Ha'aretz reporter says all of his sources show that the PRC was responsible.
Yet the PRC has denied that they were responsible. It is somewhat unusual for terrorist organizations not to race to take responsibility - on the contrary in the past we've seen multiple organizations claim responsibility for attacks even when they weren't involved.
The Israeli government would not make an explicit and specific statement without some proof. It is likely that the terrorists that were killed during the Eilat attack carried documentation that showed who they were or what group they were from, evidence that cannot be made public without compromising security.
(The conspiracy theorists can harp about how the GOI and IDF always lie and how this was an excuse to attack Gaza, but from watching their statements over the years the number of statements that they made that ended up not being true is quite small, and as far as I can tell, always a result of being pressured to make a statement before all the facts are in. And, yes, I saw the IDF spokesperson's incompetent interview.)
So why didn't the PRC claim responsibility?
The PRC has worked in the past with Hamas on terror attacks, but its main patron is Iran via Hezbollah. Its logo is even consciously based on the Hezbollah logo.IDF sources have stated that the attacks seem to have not been meant just to kill Israelis, but to kidnap an IDF soldier.
It seems likely that this is the case. Among the terror groups in Gaza, straight terror attacks against civilians has gone out of fashion due to embarrassment as these attacks go not get any sympathy from the world anymore. Since the beginning of Cast Lead, Hamas has been disingenuously claiming to only target soldiers, and the massacre of the Fogels in Itamar in March was not widely praised even by Palestinian Arabs.
In other words, the operation in Eilat was a failure.
It would have been worth it if they had managed to kidnap a soldier as they planned, because that success would have boosted the PRC stock a great deal. That success would even outweigh the chances that Israel would invade Gaza, because in the end - to them - a prisoner is worth a thousand terrorists in Israeli jails.
It seems likely that Hezbollah would have had a hand in planning and facilitating this operation. After all, although people don't remember this, months before the kidnapping of Israeli soldiers that sparked the 2006 Lebanon war Hassan Nasrallah had promised that "We are working on making this year the year to free our brothers in Israeli detention, Samir Kantar and his friends..." The kidnapping of Eldad regev and Ehud Goldwasser was planned for months specifically to engineer a release of Kntar and others. And Hezbollah planned to do more such kidnappings. This is Hezbollah's way of thinking, and from its perspective, it has worked beautifully.
The reason that the PRC refuses to admit responsibility is because it has nothing to gain by bragging about a failed operation that would end up alienating the PRC from among other Gaza terror groups who know they will pay the price of any Israeli retaliation. But if they had succeeded in kidnapping a soldier, they would be heroes, and Hamas would be the first to praise - and protect - them.
UPDATE: Zvi in the comments makes another good point: The terrorists killed a number of Egyptian soldiers, and that screw-up is worse than failing to kidnap IDF soldiers. If they take credit for the operation then they risk the wrath of the entire nation of Egypt. Read his whole analysis.