In a situation like this, you want to create an impression that you believe that you deserved the raise. At same time it is neither good manners nor good tact to not to thank your boss for the raise on the grounds that there is no favour shown. So what do you do?
In a situation you may say something like, "I am happy that you appreciate my work. Thank you." This way you are thanking him for appreciating your work and giving you something that deserve.