Arigatou pretty much just means "Thank you".
Arigatou - "Thank you" Sumimasen - "Excuse me" or a milder version of "sorry" Gomennasai - "Sorry"
If I help my Japanese roommate grab some stuff from the convenience store, he says arigatou. If he wants to really be polite he could add on "suman, meiwaku kaketa." (sorry for troubling you)
I'm not arguing against the fact that we shouldn't do literal translations between cultures, but more that you're giving misleading ideas on Japanese language.
If someone holds the door for you, or brings you a napkin, you can pretty much just say "arigatou". They will most probably just reply, "iie".
Source: JLPT N1 and member of a Japanese Teamspeak game clan for 7 years now.