The missiles seek and track based on heat differences. To an IR sensor the sky is typically pretty "cold" and just about anything in the sky is relatively "hot". Once the missile is locked onto the relatively hot signature against the cold background the sensor stares at it and adjusts the missile's trajectory to intercept it (and blow up).
Countermeasures like flares try to trick a missile's sensor into thinking the hot object it was staring at was the flare going that way and not the maneuvering aircraft going the other way. Modern IR tracking missiles try to stay locked on the object by ignoring hotter or cooler objects that might end up in its view.
At FL400+, anything not the earth is basically space – if you point an IR camera in the sky outwards, it really does look very cold as the pressure is basically zero and scattered IR photons are few and far between. Objects that are not vacuum have a signature in the IR – both a black-body temperature (which, even at ~ -55 ºC, is a hell of a lot higher than single-digit kelvin…) and possibly the opportunity to reflect any incident light.
Some modern imaging-based guidance packages for anti-aircraft missiles use multiple spectra to defeat countermeasures like flares. While a flare and a plane sometimes look similar in IR, they are easy to discriminate in the UV spectrum.
Countermeasures like flares try to trick a missile's sensor into thinking the hot object it was staring at was the flare going that way and not the maneuvering aircraft going the other way. Modern IR tracking missiles try to stay locked on the object by ignoring hotter or cooler objects that might end up in its view.