No, the existence of the JR pass exactly proves their point.
It only works on JR lines, so in Tokyo you still need to buy tickets for all the private train lines and metro lines (city run and private run). Try getting around Tokyo on the daily using only JR lines; it won't be too much fun for you.
JR pass is only really useful for long-haul, intercity type journeys, primarily by shinkansen
If you’re in Tokyo you get a suica. It works on all lines, and can also be used as a payment card at various vending machines and shops (including I think all the big combini brands and many marts).
It only works on JR lines, so in Tokyo you still need to buy tickets for all the private train lines and metro lines (city run and private run). Try getting around Tokyo on the daily using only JR lines; it won't be too much fun for you.
JR pass is only really useful for long-haul, intercity type journeys, primarily by shinkansen