The fast answer is that the protein content is the main difference.
Isolate is typically about 10% higher in protein than whey protein concentrate (90% protein vs 80% protein typically). The quality of the protein is virtually identical. The quality of the protein portion itself does not magically change in any significant way when the whey is filtered to 80% protein as compared to being filtered to 90% protein.
Whey concentrate costs less – many people use it of course.
Whey Isolate is simply regarded as cleaner and leaner (higher in protein, with hardly any (about 1-2% typically) lactose or fat remaining, whereas whey concentrate would retain about 6-8% naturally occurring lactose and 6-8% fat.