Jamison, Fausset and Brown explain John 6:49 thus:
"recurring to their own point about the manna, as one of the noblest of the ordained preparatory illustrations of His own office: 'Your fathers, ye say, ate manna in the wilderness; and ye say well, for so they did, but they are dead—even they whose carcasses fell in the wilderness did eat of that bread; the Bread whereof I speak cometh down from heaven, which the manna never did, that men, eating of it, may live for ever.'"
Clarke's Commentary on the Bible also makes this observation:
"It was an opinion of the Jews themselves that their fathers, who perished in the wilderness, should never have a resurrection. Our Lord takes them on their own ground: Ye acknowledge that your fathers who fell in the wilderness shall never have a resurrection; and yet they ate of the manna: therefore that manna is not the bread that preserves to everlasting life, according even to your own concession."
William Milligan and William Moulton (in their commentary on John) point out that Jesus' mention of the wilderness (John 6:49) is not accidental. It calls to mind verses like Numbers 14:35, which indicate that the wilderness was the place of disobedience and where obstinate men perished. Specifically, they write:
Ver. 49. Your fathers did eat the manna in the wilder ness, and died. No other bread has given life eternal. Even the manna, the bread given out of heaven, did not bestow life on their fathers, who (as the people themselves had said) ate the manna in the wilderness. It seems very probable that the addition 'in the wil derness' is more than a mere repetition of the words of ver. 31. It recalls Num. 14: 35; Ps. 95: 8-11, and other passages, in which 'the wilderness' is specially mentioned as the scene of disobedience and of death ; and thus the fathers, who (Deut. 1 : 32) ' did not believe the Lord ' and died, are contrasted with the believer who ' hath eternal life' (ver. 47). Ver. 50.
MY RESPONSE: It seems to me that Jesus' remarks in 6:31 actually follow the request in 6:28 which is premised upon the requisite works that please God. They asked for a sign because Jesus claimed to be the one God had sent (6:29). They may or may not have perceived a link between Jesus' utterance and Daniel 7:13-14. Either way, I don't see how death as punishment cannot be the issue. The "death in the wilderness" motif is cited in 1 Corinthians 10:3-5; Hebrews 3:17. Even Jude 5 refers to those males who died in the wilderness despite eating manna.