From Hiroshima to Kyoto

You are correct - you cannot use the Nozomi with the JR Pass. The trick with Hyperdia is to put in your starting & end points, then click on More Options and uncheck the box with Nozomi in it (for other routes uncheck airplane, private railway etc).
You then should get something like:

http://www.hyperdia.com/cgi/en/search.html?dep_node=HIROSHIMA&arv_node=KATSURAGAWA%28KYOTO%29&via_node01=&via_node02=&via_node03=&year=2015&month=04&day=16&hour=08&minute=00&search_type=0&search_way=&transtime=undefined&sort=0&max_route=5&faretype=0&airplane=off&ship=off&sprnozomi=off&bus=off&lmlimit=null&search_target=route&facility=reserved&sum_target=7

Hi Edward,

Toranko explained it very well.

You may also find out Planning with Hyperdia Guide useful. This explains the fine details on how to plan best with Hyperdia.

Hi Daniel and Toranko,

Thanks alot for the help provided! Now I know how to navigate Hyperdia better.

Cheers
Edward :)