They are counting that whatever disaster hits Tokyo won't hit Kyoto at the same time.
Kyoto is not without danger, as it is located downwind from the "Nuclear Ginza" (including Ooi Nuclear Power Plant and Monju) in Fukui Prefecture. For that matter, nowhere in Japan seems safe from a nuclear accident.
From Yomiuri Shinbun (5/31/2012):
皇室や文化庁 京へ移転を 首都バックアップ検討委
Capital backup committee suggests the Imperial Household and the Agency for Cultural Affairs move to Kyoto
災害時の首都機能バックアップに関する検討委員会が30日、上京区で開かれ、京都が受け持つことができる機能について、皇室の居住や文化庁の移転などとする中間報告がほぼまとまった。近く、国に提案する。
A meeting of a study committee regarding the backup of functions of the capital in time of a disaster was held on May 30 in Kamigyoku [district of Kyoto City]. The interim report was almost complete, which would include having the Imperial Household residing in Kyoto and moving the Agency for Cultural Affairs.
検討会は府や京都市、学識経験者らで構成。機能を受け入れるエリアとしては、京都市中心部と桂イノベーションパーク、らくなん進都、学研都市を対象としている。
The committee is made up of officials in Kyoto Prefecture and Kyoto City and persons of experience and academic standing. The areas that would host the backup functions would be Kyoto City center, Katsura Innovation Park, Rakunan Shinto, [Kansai] Cultural and Academic Research City.
検討会では、京都は首都圏と同時に被災する可能性が低く、地理的にもアクセスしやすい利便性があることを確認。その上で、京都御所や京都迎賓館があることから、皇室の人々の居住や儀礼の実施を受け入れやすいと判断した。また、文化庁や観光庁の移転、国会や首相官邸の代替施設となる可能性があるため国立京都国際会館の機能を強化することも国に提案する。
The committee acknowledged Kyoto to have a low possibility to be hit by a disaster at the same time as the Tokyo metropolitan areas, and to be easily accessible geographically. In addition, the existence of Kyoto Imperial Palace and Kyoto State Guest House makes it easier for the Imperial Household to reside in Kyoto and conduct ceremonies. The committee will suggest to the national government to move the Agency for Cultural Affairs and Japan Tourism Agency and to strengthen the Kyoto International Conference Hall to serve as the National Diet and the Prime Minister's Official Residence.