Congress did not intend that the Roth IRA, given the rather low annual contribution limit, would allow someone to accumulate essentially unbounded amounts of gain in a tax-free way.
If you read up on what Thiel (and presumably some others did), yes, they successfully invested using their IRA, but yes, they also took advantage of the tax status of a Roth to avoid paying capital gains tax.
They will not be retroactively penalized for this (the law doesn't work this way), but their doing this has now made at least some in Congress want to prevent this from being possible in the future, since it was not what the Roth IRA was intended to allow.