Given the massive amount of IRS shenanigans over the years, it is easy to imagine certain groups unfavored by the government conveniently being led to file returns that cause them to miss out on subsidies they are actually eligible for, or to pay higher taxes based on filing their return in correct but unfavorable ways resulting in higher tax payments than necessary.
This risk is particularly high given that the program was intended for and marketed to low income filers who typically rely on their tax preparer as an advocate to ensure their tax payment is as low as legally possible.
As other comments have mentioned, the program also exceeded statutory authority. Congress authorized the IRS to study a direct file system, not implement one on a permanent basis. It is a good thing when our government is restrained after it oversteps legal boundaries.
This is especially true in the case of this program because it was being intentionally implemented on a massive scale in order to make it politically unpopular to shut down. A program that allows 10% of all tax payers in 25 states is obviously much more than a study.