Matsusaka to toba - how to go - no jr rail

I checked hyperdia and it looks like Matsusaka to toba is only via kinetsu. Osaka to Matsusaka is also only via kinetsu. Does this mean I can't use my jr rail pass?

Please advise if I am doing the search correctly.

Both Matsusaka and Toba stations are also served by JR, but the trip with JR takes longer than with Kintetsu, which is why Hyperdia is not displaying JR options. You can uncheck the "Private railway" box to show only JR.

Your search is not correct!

Matsuzaka and Toba are also connected by JR trains:
http://www.hyperdia.com/cgi/en/intervaltime.html?dep_node=MATSUSAKA&ar...

Osaka to Matsusaka is also only via kinetsu.

The most direct line is Kintetsu, but with a detour you can also make the trip by JR. If you use the shinkansen via Nagoya, it is not much slower. But note that there is a small non-JR section between Nagoya and Matsusaka for which you will have to pay a small supplement (510 yen).

why Hyperdia is not displaying JR options

Or at least not always, depending on your search date and time.

The map here may be useful, by the way: http://japan-guide.com/list/e1105.html

Matsusaka is at the intersection of the JR (yellow) and Kintetsu (green) lines, a little bit south of Tsu.