This is not a problem. If cryptocurrencies become widely used and the associated business accumulate significant market value, major market indices will rebalance in such a way to include cryptocurrency businesses and the passive index investor will be fine.
In fact, it doesn't matter if the future is in crypto, plastic or tulips; equity index investors will be fine.
Basically, the index fund itself becomes a bet that the future will look much like the present, at least qualitatively, and that future investors will demand the same categories of securities as present ones do. If the future looks dramatically different from the present, then people who bet correctly with their particular version of the future reap the spoils, at the expense of all index fund investors.
(I should note that this is explicitly the purpose of indexing - by giving up the possibility of above-market returns and settling for market returns, you can eliminate the need for fees. If you believe that being average is good enough, this is a good bet. If you believe that the average person is going to get screwed and bad financial things will happen to the lots of people, why would you want to be them?)
More likely they will buy new crypto focused companies (Coinbase IPO) or that existing firms will adopt crypto based business lines. The investment is firms innovating, rather than the value of the underlying instruments or technology they use.