Tokyo to Odawara
Yes, you can use the JR Railpass to get to Hakone. The JR Railpass will allow you to ride the shinkansen bullet train to Odawara Station. All shinkansen do not stop at Odawara so make sure you catch the Kodama shinkansen. The shinkansen ride from Tokyo to Odawara is only about 40 minutes. At Odawara station it is an easy transfer to the Odakyu Line train which will take you to Hakone Yumoto Station on a 15 minute train ride.
You can also take the normal JR Tokaido line as well from towns like Yokohama, Atami, or Kamakura.
Odawara is also worth some time to explore the beautiful castle, morning fish market, zen temple, or traditional foods like kamaboko.
The Odakyu Freepass is a wonderful option for the Hakone area. It can be purchased at Odawara or Hakone Yumoto Stations. This pass will give you the ability to ride the buses, boats, ropeway, and mountain train all on one ticket.