Where to stay in San Francisco?

What area of the city is best to stay as far as safety, central location for walking, trolley, etc? We are flying in on a Thursday morning, plan to do Alcatraz, see the city, stay that night, hang in city most of Friday and then need to leave Friday evening to make our way to Humboldt. It will be 2 adults and 2 kids (17 & 11). Oh and how do you take the trolley? Do you need Tix?? TIA!