Of course airlines are running a business with the aim of making money. Frequent flyer programmes are, for some airlines, a bigger money machine than the actual business of flying nowadays. This goes far beyond enticing customers to purchase tickets on their airline - this is about the business of buying and selling miles/points as currency. And in that game the FFP is the bank - and the one who decides the value of the currency. They sell their points to partner airlines, as well as Visa/MC/Amex for real cash. And only have you spend those points on a service that hardly costs them anything (i.e. seats that would otherwise go unsold). And of course depreciate the value of points when it suits them. Its a game that they know to play very well.
Having said that I do not believe that, as an individual, taking part in that game is a bad thing. When played correctly there is still value to be gained. It's important to not let yourself be blindly guided by what the airline or FFP tries to have you do. But when you understand the game there is nothing wrong with taking part. Just be aware of the decisions you are making.
So practically that, typically, results in a few general guidelines: Book the cheapest flight that suits you, in the lowest class that suits you, on any airline. Don't value earning miles and points at something higher what you can actually spend them for. And...spend your points. Devaluation is an ongoing thing, so don't keep them sitting in your account. Spend them because their value will only go down.