Is what atheists say true, that bird droppings on the Kaaba indicate that God does not protect His House, and how do we respond to them?

We have not seen the video in question, but bird droppings are pure and there is no issue with them. Birds glorify and prostrate to Allah, unlike atheists. Atheists are like "cattle, nay, they are even more astray" because they do not benefit from their intellects, thus neglecting faith in Allah and obedience to Him. An atheist is someone whom Allah disgraces. Had Allah willed, He would have prevented the bird. Whoever doubts Allah's power is mentally unsound. Allah challenges the atheist with death, from which there is no escape.

The questioner should learn her religion and its fundamental rulings before occupying herself with the شبهات (doubts/specious arguments) of atheists. She does not possess sufficient knowledge to refute these شبهات, and her current state indicates doubt and misguidance. It is advised to abandon such شبهات and to delve deeply into understanding Islam and its proofs, and to enroll in programs or academic courses that refute atheism to strengthen her faith and avoid perdition.