As a couple whose chances of conceiving are, naturally speaking, all the time, low or near to impossible, do not sin if they continue to have marital relations, provided the secondary ends are always subordinated to the primary, a fortiori a couple whose chances of conceiving are, naturally speaking, during a particular time, low, do not sin if they continue to have marital relations during that time, provided the secondary ends remain always subordinated to the primary. So, NFP certainly isn't intrinsically evil, as contraception is.
In the Holy Bible, God Almighty strikes Onan dead for practicing contraception. Gen 38. Some forms of contraception were called Onanism historically just as some forms of the sin of sodom were named after that city that was destroyed in fire. Also, it is worth noting that every form of perverted sexual relations, so widely promoted today in every way, are all intrinsically contraceptive and closed to life.
A confessor's advice should be sought to see in the concrete case if sufficiently grave reasons exist to have marital relations only during infertile or near to infertile times. As others mentioned, the Rhythm mentioned involves nothing more than periodic continence. Those who wish to argue that that is wrong must prove (1) either that complete abstinence is wrong, or (2) that couples are bound to have marital relations only on days of normal or maximum fertility. Some couples indeed do that, to maximize chances of conceiving, but clearly periodic continence cannot be per se wrong in itself, unless either continence itself is wrong, or one is bound to (2). So, it is not intrinsically wrong, but it is wrong, by the doctrine of double effect, to practice it without a sufficiently grave reason, which DE requires.