CyanogenMod, one of the most popular alternative Android ROMs available for Android powered devices will now ship with root access disabled by default. CyanogenMod explained in a blogpost that due to the security concerns posed by the root access they enhanced the security by merging 3 patches into CyanogenMod 9.
CyanogenMod 9 alpha builds now come with root access disabled by default, but users can configure if they want root access. Users can configure to enable root access for ADB only, or for Apps only or for both ADB and apps only.
By addressing the change CM team says shipping root enabled by default to 100,000+ devices is a security risk, so they introduced user configurable options, that way advanced users can access the root while other users are secure by turning off the root by default. As the CyanogenMod becomes more mainstream with lot of users unaware of the dangers posed by the root access it is necessary to keep these checks.
Source: CyanogenMod