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Definitely more convenient generally (particularly if journeys involve transits between different forms of transport) and if you plan to take a golden gate ferry (eg to Sausalito) it's a no brainer (from memory cash fare around $11, clipper fare around $5 plus clipper card purchase for $3) - the saving pays for it straight away.
If wanting to travel on cable car multiple times on a day consider a Muni day (or multi day) visitor pass. Not sure if these can be loaded onto a clipper, I am sure though googling this will get an answer.
Some cut and paste that might be useful Passport can be bought as paper passports or can be bought as a Clipper passport ($3 more) - see below
We bought the 7 day clipper passport as we bought it from the vending machine, you need to go to a counter to get the paper version if that is still available.
Yes, you can use it on the cable car for unlimited rides for the no of days you bought them
Single cable car ride is $6! so a no brainer if you are going to take it a few times.
Passport prices have gone up from 1st Jan...
If you want to take non passport included trips you will need to either buy single trips or get a clipper card/passport and load it with $$
(we did the single trips option as most of our transport needs were met by the passport)
Whether you're here for a day or for several weeks, SFMTA makes it simple for visitors to get around the city with ease. A Visitor Passport can be purchased for 1, 3, or 7 consecutive days of unlimited rides on Muni, Muni Metro, historic streetcars, and cable cars.
If you intend to take the cable cars and other public transportation often, it might save you money if you purchase a "passport." There are three different passports: 1-day, 3-day, and 7day. Passports can be purchased at the Visitors Information Center before the urban trek and at other locations (refer to link below). IMPORTANT NOTICE: In my opinion, it is not worth getting the 1-day passport if you will not be taking the cable car that day. Right now, a 1-day passport is $15.00 and bus fare is $2.25 for adults with 90-minute transfer privilege. To make it worth the price, you will have to ride buses constantly for more than 10 hours in one day. A 3-day and 7-day passport could be more economical if you will be staying 3 days or 7 days, respectively.
Here's a link to passport information: http://www.sfmta.com/getting-around/transit/fares-passes/visitor-day-passes
Warning for Muni passport - If you go to a Walgreens to purchase a Muni passport these days, they will usually give you a Clipper Card and charge you $3.00 extra for each one. Therefore, it is better to purchase the paperMuni passport at other locations so you do not have to pay the $3.00 additional fee.