Recently (not sure the exact date), Apple started disabling certain Safari plugins by default. That's great for security, but it's not that great for usability, especially if users actually want to use those plugins.
If you want your users to enable plugins themselves manually, they can follow Apple's instructions at How to use Internet plug-ins in Safari for Mac.
If you'd like to deploy a .mobileconfig profile, though, I've posted a sample one on GitHub that enables Flash, Java, and Silverlight (ask first, not just on all the time).
Rod Christiansen has a more comprehensive sample up (more plugins).
In addition to the plugins being generally enabled or disabled (with 0 or 1 / false or true), there is also a first-visit policy to look at.
This is the default setting (blocking):
This is the setting in the profiles I linked to:
And this is if you want it on (not asking):