Is "to fight with" ambiguous?

I've read about a Dutch volunteer, who died in Syria "fighting with the rebels". Obviously from the context you could understand, that he was fighting for the rebels, against the government troops. Article was written by non-native speaker.

Is "to fight with" ambiguous and can be used both as "to fight for" and "to fight against"? Or is is unambiguous and only "to fight against" is the only valid interpretation?

Yes, to fight with is potentially ambiguous.

For example, most if not all of thousands of written instances of fought with the French Resistance will mean on the side of / alongside the Resistance.

On the other hand, most instances of fought with the devil will mean against the devil.

If there's any danger of being misunderstood, you can always just use alongside or against to make things crystal clear. But usually the context makes the intended meaning obvious.

Also note that if you don't use any preposition at all (fought the French resistance), it always means against (there are only two of those, because it's not a very common thing to say).

In a word, yes, it is ambiguous. "Fight with" can refer to either fighting against, or fighting for. Think of the phrase "fight with" as simply a statement that two parties are fighting in the same battle. This doesn't say anything about what side of the battle either side is on.

It is worth noting though that "fight with" usually only refers to arguments and squabbles, normally only between two people. In the context of a military confrontation, it is more likely implying that the two were on the same side (i.e. the Dutchman was on the side of the rebels, in this case).