Hi Glo,

Toilets are the dwelling places of evil jinns. They like sticking around in unclean places such as toilets and dunghills etc. Since toilets are a place where we deposit dirty smelly bodily waste, they also retain that sense of uncleanliness in the psychological sense. I'm sure no one would like to eat dinner in one no matter how clean it was :P

The Prophet (PBUH) also advised us to seek protection before entering the toilet.
Anas ibn Malik (may Allah be pleased with him) who says: “When the Messenger of Allah (peace and blessings be upon him) entered the toilet, he would say, 'Allahumma inni a`udhu bika min al-khubuthi wal-khaba’ith (O Allah, I seek Refuge with You from all offensive and wicked things [evil deeds and evil spirits]).'”

I suppose the presence of filthy jinns also contributes to them being unclean places. That's all I can think of Glo. I hope that helped