Sampdoria scored their goal from a penalty awarded for handball by Aleksandar Kolarov, a decision the referee made after reviewing the incident on a pitch-side video screen.
However, Roma believe they should have been awarded a free kick for obstruction on Kevin Strootman in the build-up.
"The VAR system should protect the teams, but it needs to be the same for everyone," Di Francesco told reporters.
"My verdict? There are fewer protests and fewer sendings-off but (referees) are continuing to make mistakes, so from that point of view, I'm not in favour."
Di Francesco became the latest coach to question they use of VAR which is being tested in Serie A this season as well as other leagues around the world.
Soccer's rule-making body IFAB is due to decide in March whether to approve its use on a permanent basis and global soccer body FIFA wants to use it at the World Cup in Russia.
"We fell behind in the first half following a situation that I don't think was right, You have to assess everything in these cases," Di Francesco added.
"In football that's called obstruction. If you show no interest to get the ball, it's a foul. The worst thing is that the linesman raised his flag and he was ignored. If that wasn't obstruction, I don't know what is."
Lazio coach Simone Inzaghi has said that VAR is taking the enjoyment out of the sport and Juventus boss Massimiliano Allegri commented that matches could last three or four hours if referees did not change the way they used it.
(Writing by Brian Homewood in Bern; Editing by John O'Brien)
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