Well for one they seem very confident in taking it to both the CAS and wider than that to the European court if that fails (which seems to be reported). They will be getting advised by top legal people, and they wouldn't be pursuing that avenue if they didn't feel there was a chance of winning.
More broadly though, because FFP is a poorly designed set of rules that is in breach of many of the founding principles of European law. In spite of the PR job currently being done in the press for FFP it is a set of rules that bakes in inequality. There also seem to be aspects of the law that infringe upon shareholders rights to spend the money as they choose (which again is frowned upon).
Think of it this way, imagine if tennis introduced a set of rules that formally allowed one player to spend more money on training, or use of facilities, or air travel than another player. Then imagine the 2nd player spent the same as the first on air travel (so bought himself a 1st class ticket). Then the governing body of tennis said he couldn't do that, because he wasn't as successful as player 1, and fined him/restricted his opportunities. They would have a very clear case to be had legally, irrespective of what the rules say. That is the essence of what FFP allows. It allows for some companies to spend more money than others. This fails the anti-competitive test.
The reason why it's murky with City is (from what I can see)
1) Made very elementary mistakes
2) Are being charged it seems for lying on their accounts as opposed to the level of infringement.
3) There is a whistle blower that is strengthening UEFA's hand.
If the case is that City have fabricated accounts, and this can be proved, then a lot of the above I have mentioned isn't strictly relevant. City could argue that the fabrication was as a result of the flawed set of rules, but thats in no way a given that the law would side with them. It could go either way.
They also seemingly have Sheikh Monsours fingerprints all over the transactions, as opposed to a company's. So again, the position that this is an infringement of a company's (or it's shareholders rights) to spend what they wish on what they wish is lost. UEFA are in quite a strong position to say it's not a company, it's an individual, the same individual that owns the club. While it's a grey area, there is far more scope that allows games to limit the amount of investment single individuals can make into a sport to make it fair.
There is a lot of points and counter points in this. It's worth noting City are challenging most of what UEFA are saying, and we may only begin to see the true state of play once we move into an impartial court. However that would be my reading of it above. In a broad sense City have a great chance, as FFP is flawed on a number of levels, but their specific case looks pretty weak.