He was probably the 6 yr old son in the 1861 census transcript I gave you, and known by his second name Thomas (this happened quite often in my IOM families):
1861 Braddan Awhallan: Philip Cain 58 Labourer, wife Cathrine Cain 50, and sons Philip Cain 24 unm Shoemaker, and Thos Cain 6 Scholar. All b.Braddan.
I can't see a son bapt with those parents who has a first name Thomas [in IGI].
Have a look at Brian Lawson's census index, to look at alternatives:
Cain was such a common name in the IOM that it might help if John/Thomas can be found in later censuses. Who did he marry, and where was he living?
Sometimes relatives were visiting at the time of the census.