Reasons
The Pirkei D'Rabbi Eliezer (34) explains that when a fruit tree is cut, it cries out so loudly that the sound is heard from one end of the world to the other, although it is not captured by the human ear. The Medrash in Bereshis Rabbah (13:2) learns from the pasuk: “Now no tree of the field [siach hasodeh] was yet on the earth" (Bereishis 2:5) that the trees lesochaiach – ‘talk’ to the creatures, and were created for human pleasure. The Medrash continues and tells of a person who was harvesting his grapes in his vineyard and fell asleep there. A spirit came and harmed him there.
The Ohr Haskel and Yedi Moshe explain that this person didn’t endanger himself by sleeping alone before cutting down his vines, although sleeping alone is considered a danger, because vines speak amongst themselves and he was not alone. Only once he cut the vines was the spirit able to harm him. Interestingly, modern research has shown that speaking to plants helps them grow better. This shows the energy of plant life – an energy that allows plants to express themselves and retaliate when harmed.
The Radal explains that this was the 'language of palm trees' that Rabbi Yochanan ben Zakai understood (Succah 28a). The Arizal provides a kabalistic interpretation for this halachah: The trees have reincarnated souls in them and when the tree is cut down, those souls do not reach peace and subsequently they bring about danger.
An additional reason is found in the Sifri (Shoftim 203): Since trees give humans life, it is improper to cut them down. Wheat, too, falls into this category and therefore the Magen Avraham writes (Zayis Ra'anan 247:923) that the prohibition includes wheat.
The Sefer HaChinuch explains (Mitzvah 529) that righteous people live peace and rejoice seeing goodness in the world, bringing them closer to Torah. Righteous people find value in everything Hashem made and will not waste even a grain of mustard, feeling real pain over every loss and waste that they see. If they can only save something from waste, they will do everything they can to prevent the loss. Evil people are, contrarily, lovers of destruction. They rejoice with everything that spoils or ruins the world and they destroy everything they find. The Sefer HaChinuch explains that the results are measure for measure. One who wishes to see the world grow and flourish connects himself to the attributes of good and rejoicing of the soul. However, those who lean towards destruction allow this attribute to cling to them.
