This is an interesting article on the "feud" that has often been put forth as why many of Hatshepsut's monuments were destroyed. This is a major issue for Ancient Egyptians as they believed that this is how the Pharoah lived on in etnerity and to destroy their statues and writings (so their memory) was to destroy their soul in the afterlife. The bulk of the destruction was done during her stepson, Tuthmosis' reign, and so many assumed that he hated his stepmother for taking some of his power (as she ruled as co-regent). Dr. Joyce Tyldesley has this to say on Tuthmosis:
It is undeniable that someone attacked Hatshepsut's monuments after her death. Archaeology indicates that the bulk of the vandalism occurred during Tuthmosis' reign. Why would he do this? At first it was imagined that this was the new king's immediate revenge against his stepmother; he was indeed cursing her with permanent death. The image of the young Tuthmosis seething with impotent rage as Hatshepsut ruled in his place is one which has attracted amateur psychologists for many years. However, it does not entirely fit with the known facts.
Tuthmosis was to prove himself a calm and prudent general, a brave man not given to hasty or irrational actions. He did not start his solo reign with an assault on Hatshepsut's memory; indeed, he allowed her a traditional funeral, and waited until it was convenient to fit the desecration into his schedule. Some of the destruction was even carried out by his son, after his death, when most of those who remembered Hatshepsut had also died. It is a remote, rather than an immediate, attack.
Furthermore the attack is not a thorough one. Enough remained of Hatshepsut to allow us to recreate her reign in some detail. Her tomb, the most obvious place to start the attack, still housed her name. Hatshepsut may have been erased from Egypt's official record, but she was never hated as Akhenaten 'The Great Criminal' would later be.
So what does she think happened?
What can we conclude from this tangled tale? We should perhaps rethink our assumptions. Hatshepsut did not fear Tuthmosis; instead of killing him, she raised him as her successor. Tuthmosis may not have hated Hatshepsut. Initially he may even have been grateful to her, as she had protected his land while training him for greatness. But, as he grew older and looked back over his life, his perspective would shift. Would Egypt's most successful general, a stickler for tradition, have wished to be associated with a woman co-regent, even a woman as strong as Hatshepsut?
By removing all obvious references to his co-ruler Tuthmosis could incorporate her reign into his own. He would then become Egypt's greatest pharaoh; the only successor to Tuthmosis II. Hatshepsut would become the unfortunate victim, not of a personal attack, but of an impersonal attempt at retrospective political correctness.
Tuthmosis set his masons to re-write history. Their labours would last well into the reign of his successor, Amenhotep II, a king who could not remember Hatshepsut, and who had no reason to respect her memory. Meanwhile, hidden in the Valley of the Kings, Hatshepsut still rested in her coffin. Tuthmosis I had been taken from their joint tomb and re-buried, but she had been left alone. Tuthmosis knew that as long as her body survived, Hatshepsut was ensured eternal life.
I find this story - that Tuthmosis was trying to improve his image - as more pausible. It makes sense with the partial destruction and shows that while he was trying to negate her role, he wasn't trying to kill her memory - merely change it to suit himself.