Shiluach HaKein - And do Mitzvot Have Reasons?

(6)If, along the road, you chance upon a bird’s nest, in any tree or on the ground, with fledglings or eggs and the mother sitting over the fledglings or on the eggs, do not take the mother together with her young. (7) Let the mother go, and take only the young, in order that you may fare well and have a long life.

It is also prohibited to kill an animal with its young on the same day (Lev. 22:28), in order that people should be restrained and prevented from killing the two together in such a manner that the young is slain in the sight of the mother; for the pain of the animals under such circumstances is very great. There is no difference in this case between the pain of man and the pain of other living beings, since the love and tenderness of the mother for her young ones is not produced by reasoning, but by imagination, and this faculty exists not only in man but in most living beings.

The same reason applies to the law which enjoins that we should let the mother fly away when we take the young. The eggs over which the bird sits, and the young that are in need of their mother, are generally unfit for food, and when the mother is sent away she does not see the taking of her young ones, and does not feel any pain...

MISHNA: One who recites in his supplication: Just as Your mercy is extended to a bird’s nest, as You have commanded us to send away the mother before taking her chicks or eggs, so too extend Your mercy to us; and one who recites: May Your name be mentioned with the good or one who recites: We give thanks, we give thanks twice, they silence him.

This also is an explanatory commandment, of the prohibition ye shall not kill it [the dam] and its young both in one day, because the reason for both [commandments] is that we should not have a cruel heart and be discompassionate, or it may be that Scripture does not permit us to destroy a species altogether, although it permits slaughter [for food] within that group. Now, he who kills the dam and the young in one day or takes them when they are free to fly [it is regarded] as though he cut off that species.
Now, he [Rabbi Moshe ben Maimon] wrote in the Moreh Nebuchim...

And so too what was written in Brachot, it assumes the middot of Hashem to be mercy and not decrees, to say we should have mercy on the birds but not have mercy on sacrificing the parent and son on the same day, as his mercy does not address all lifeforms to prevent us from utilizing them, for if that were the case slaughtering would also be assur, but the reason for this mitzvah is to teach us the attribute of mercy, not to be cruel. Because cruelly stupefies the man, as butchers who slaughter large animals are cruel individuals as it states butchers are the partners of amalek. And so the mitzvot by animals and birds are not to have mercy on them, rather decrees on us to guide and teach us good traits. ​​​​​​​

Honor your father and your mother, that you may long endure on the land that your God ה' is assigning to you.

One ought to consider the laws of the Torah and to penetrate into their ultimate significance as much as he can. If, however, he cannot discover the reason and is ignorant of the basic cause of a law, he should not regard it with contempt.