In case you are referring to LT or LV ( LOW TENSION or LOW VOLTAGE upto 440V ) capacitors, a switch fuse or a circuit breaker are equally effective for isolation or protection. Cost is usually the consideration.
Personally I would prefer switch fuse because if one fuse blows, the remaining 2 healthy fuses will keep the capacitor partly effective in improving the power factor.
A circuit breaker or switch fuse cannot really protect the capacitor against age related damage or deterioration. Only if you use voltage sensing relays, you can put a circuit breaker to good use in protecting the capacitor ( but you will face drop out of capacitors at awkward times thus lowering PF and raising Maximum Demand )
Finally, if you are referring to high voltage capacitors ( 11 / 22 / 33 kV ), circuit breakers are the only option as the arc during closing and opening is very severe.