It's not difficult, although it can be time consuming - Israeli security is very thorough. There are bus services which will take you to the crossing, then there's a short walk involved to get to buses to take you to Jerusalem. It's possible to get a ticket to take you the whole way - you won't be on the same bus, so it means carrying your luggage for a while, but they operate like shuttles. Getting a taxi is a pretty affordable option, lots of companies will let you pre-book.
As you go through Israeli immigration just check what type of entry visa they give you, for some unknown reason they give some travellers a "west bank only" visa (even if they have no Arab heritage) which restricts your travel in and around the West Bank. Insist on a full visitors visa, but do it nicely - they're usually armed. almost 7 years ago