I think that's interpreting too much into the comment, especially with the reference to Poland and Hungary: It's saying that if the governments cause problems with EU law, the commission has tools to handle that. The commission does not have the power to just cut funding without a reason, and if it ever attempts to do so the EU courts will put a stop to it. The treaty violation processes are slow, intentionally. (And the majority of member states is quite happy with that, since most of them run into that occasionally, and also has all the reasons to not stand for that)

"We'll pay close attention if you stick to the laws" is pretty much the worst the commission can really threaten a government, which isn't really all that much if there is nothing serious to punish.