The main reason is that he was the person who "abolished" (in quotes because it wasn't directly his fault) the Ottoman Empire, which was the last legitimate Caliphate, or Islamic Government. The Caliph in Islam is much like a Pope in Christianity. Imagine the Papacy was abolished today-- the controversy would never end.

Another reason is that majority of Turks are Muslim, and many Turks "worship" Ataturk by hanging his pictures everywhere and revering actions, when he was an alcoholic and critisized religion while he was raised a Muslim himself.

I have no religion, and at times I wish all religions at the bottom of the sea. He is a weak ruler who needs religion to uphold his government; it is as if he would catch his people in a trap. My people are going to learn the teachings of science. Let them worship as they will; every man can follow his own conscience, provided it does not interfere with sane reason or bid him act against the liberty of his fellow man.

Ruşen Eşref Ünaydin, 1954, "Atatürk -Tarih ve Dil Kurumları Hatıraları" Türk Tarih Kurumu. page 28-31.

Meanwhile, he forced women to remove their hijabs and banned the wearing of one, as well as banning the wearing of fezzes or turbans.

http://tr.wikisource.org/wiki/%C5%9Eapka_%C4%B0ktisas%C4%B1_Hakk%C4%B1nda_Kanun