Reason #1 one why we like Phantom better than Raoul: The Phantom sings Music of the Night, one of the most beatiful songs I have ever heard.
Reason #2: He seems to love Christine more passionatly than Raoul does.
Reason #3: He's, technically, the villian. ;)
Reason #4: In the end (sorry if this spoils it for some of you...) he lets Christine go with Raoul.
Reason #5: He's mysterious.
Reason #6: He tries to help Christine's career flourish and bloom so she's happy.
Reason #7: He sings better than Raoul.
Reason #8: Lots of people like Phantom more than they like Raoul.
Reason #9: His costume in 'Masquerade' kicks butt.
Reason #10: He's the Phantom of the Opera.