"Bom dia, doutor!"
Translation:Good morning, doctor!
Yes. Good morning would be literally "boa manhã", but in the morning in Portuguese language we wish the person to have a nice day, so we say "bom dia"
Yes, it can mean a medical doctor or someone with a Phd from University. http://dictionary.reverso.net/english-portuguese/doctor
"Médico/a is a doctor of medicine. Anyone with a PhD can also be a doctor (doutor/ra) such as a Doctor of Philosophy = *Doutor de Filosofia" (where the PhD abbreviation derives).
A doctorate degree is the one above a master's degree which is above a bachelor's (or baccalaureate) degree which is above an associate degree.
So, someone can be a "doctor" (even using it in their name as Dr. as an honorific in place of Mr/Ms, but not all are medical doctors.
Other honorifics (and doctorate degrees) usually placed at the end of names to eliminate ambiguity are MD (Medical Doctor), DC (Chiropractor), ND (Naturopathic Doctor), OD (Optometrist) JD (Doctor of Law), EdD (Doctor of Education), DTh (Doctor of Theology) and so on: