The FLAC-to-Ogg mapping page has a fairly thorough explanation of why it's desirable to use Ogg encapsulation in many cases instead of streaming native FLAC:
The original FLAC format includes a very thin transport system ... known as 'native FLAC'. ... It is very lightweight and does not support more elaborate transport mechanisms such as multiple logical streams, ...
The native FLAC transport is not a transport "layer" in the way of standard codec design because it cannot be entirely separated from the payload. ...
This presents a problem when trying to encapsulate FLAC in other true transport layers ...
The alternative is to treat native FLAC frames as Ogg packets and accept the transport redundancy. It turns out that this is not much of a penalty; ... The redundancy amounts to a fraction of a percent.
[emphasis added]
See the complete page for more information, but the upshot is that while usable for streaming, native FLAC isn't well-suited to more complex setups and the cost of Ogg encapsulation is quite low. If native FLAC works fine for your specific needs, you can go ahead and use it, but Ogg will ultimately give you more flexibility.