The US and Turkey are in the process of training what they envision will eventually be a significant rebel force for Syria of thousands of pro-US rebels. Who are they rebelling against? That’s a subject that is going to be more and more important as the training progresses.
It’s also something the Syrian government is watching closely, and their foreign ministry is warning reports that the US has agreed to provide them air support in their rebellion is de facto aggression against Syria.
They may not be wrong. The US has made much of the idea that these rebels will be fighting against ISIS, but being rebels there is also an understanding that they’re going to eventually be fighting the Syrian government as well.
Turkey has been pushing for regime change for years, and their efforts to get this concession from the US also included attempts to get them to declare a nationwide “no-fly zone.” That’s obviously aimed at Syria, not ISIS, since ISIS isn’t the one with an air force.
But so long as the US presents the air support as preventing the rebels from getting routed by ISIS, they are likely to be able to sell the plan as not overt aggression against the government. That said, it will almost certainly become so in the future.