Although our observance of the Torah is irrespective of our ability to fathom the reasons of the all-wise Creator in directing us in a particular way, nevertheless, there is a need to explain why a wise, rational, loving God would impose such restrictions on something so "natural." What are the benefits? Why did God command this behavior? What insights are to be gained from these laws?
The divinely commanded periods of sexual abstinence should prompt us to consider that there is much more to marriage than sex. The most meaningful part of the marriage is the loving, considerate relationship between two people who care for one another and assist one another on their life's journey--sharing happiness and grief; together experiencing life's ups, downs and in-betweens; communicating deepest emotions and highest aspirations. The loving relationship is so much more important than sex--existing even when sexual expression of this love does not. The periods of sexual abstinence shut out the overwhelming thunder of sex, so that the subtle, soft music of relationship can be heard. Once the music is heard you know it is always there even when the sexual expression of love is again permitted.
In general, the laws concerning controlled sexual behavior can be subsumed under laws of holiness. Holiness in man is founded on the deep- seated belief that there is more to man than the physical and that man's behavior should aspire to the highest ideal of God-like behavior.
Holiness of the marriage takes the position that there is much more to marriage than the physical sexual relationship between husband and wife. The physiological and emotional power of the sexual relationship threatens to overwhelm what is ultimately and logically the most important part of the marital relationship--the mutual respect, sensitivity, concern and giving of two people who have become as one. (Upon going to the doctor a pious person of Jerusalem said: Doctor my wife's foot is hurting us.) Holiness of the marriage requires the putting of the sexual aspect of the relationship in perspective by having periods where it is non-existent. The onset and the duration of these periods are not determined by one or the other partner, a situation which could lead to resentment, but by a non-volitional "natural" event--menstruation. The periods of abstinence are a time for the couple eager to express there continued relationship, to focus on and develop other means of expressing the depth of their relationship.
Another, physiological, basis for the laws of niddah might be culled from the recent work of biological theorists who have proposed the following "reason" for menstruation. Being as the uterus is subject to intrusion of elements foreign to the woman's body, the lining of the uterus is sloughed off periodically in order to flush out foreign elements which might have entered the woman's system. Since the sperm can be a vehicle for the entrance of foreign elements (bacteria, viruses and the like) it makes sense biologically for the couple to prevent the entrance of sperm during this changeover period.
While these might be some of the reasons for the laws of niddah, it is unlikely that we could even begin to understand the will of our Creator. Ultimately it is our belief that Hashem is "abundant in loyalty and faithfulness" ("rab hesed ve'emet") which demands an absolute adherence to even the smallest nuance of His Law.