Only the Note rate is the rate you will have. For APR, it's used for the borrowers to compare which rate is better for them.For example, 5.5% with 2 points, and 6% with zero points, both for 30 yr fixed. A lot of people can not tell which one is better, compare APR will help.
But is APR lower the better? Not necessary. For the above example, you may have 5.75% APR with 5.5% plus two points, and 6.14% with 6% and 0 points. Unless you stay there long enough, then the first option is better.