Specifically they are that:

1. The layout of the dashboard is different

2. Only funnels have the ability to:

a) Redirect forms/calendars/surveys to a 'next step'

b) Use order forms to sell products and services

So one common use of the two areas is to have your main website in the 'website area' and the 'opt-in' or 'sales' funnels built in the 'funnel area'.

Remember you can also used 'saved sections' from the website pages in the funnel pages and vice versa!