I have had a look through the census returns that cover Rhydymain but I couldn't find a Rev J Jones there.
Unfortunately with a name as common as J. Jones it is difficult to suggest where else he might be.
One of the problems with finding ministers is that they tend to work on Sundays, and censuses are collected on a Sunday. The Rev J. Jones might have had a preaching engagement anywhere in Wales (or in one of the English cities that had a Welsh Chapel) so he might be recorded as a "visitor", "lodger" or " boarder" in any number of places away from his own chapel.
Until the 1880’s many Welsh ministers weren’t paid a stipend for their ministry, they were paid for preaching and other services on a "piece" basis, so they had other jobs in order to guarantee a regular income. John Elias and Thomas Charles were both shopkeepers, John Jones of Talsarn was a mine worker, many ministers were farmers; so your Rev J. Jones may be recorded in the census by his day job rather than by his ministry.
Some of the smaller villages and hamlets, such as Rhydymain, shared a minister with neighbouring chapels. It might be worth extending your search for Rev J. Jones to neighbouring places such as Brithdir, Bryncoedifor (hamlets in the parish of Dolgellau), the town of Dolgellau / Dolgelley, Llanfachreth village, Llanuwchllyn etc.
There is quite a lot of peripheral information available about ministers; in chapel records for example; in the 100’s of “Biographies and Collected Sermons” of dead ministers written in the late 19th / early 20th centauries. But with just the Rev J. Jones it is difficult to suggest the best way of furthering your research to see if any of these sources may help.
As you only give an initial, I assume that you don’t know much about your Rev Jones, but you MUST have a little bit more information than just his initial and his surname – otherwise you wouldn’t be looking for him – can you tell all that you know about the man – even the slightest detail might help find him amongst the thousands of other J. Joneses who lived in Wales in the 1870’s