Let's take some time to explore various songs, and the approach the guitarist takes in each. There are several philosophies of playing funk rhythm guitar....
Minimalist Funk & Funk Guitar
Often somewhat misleadingly referred to as "black funk" (because, initially, more African Americans took an interest in this approach to funk music), the concept here is "play what you need to play, and get out of the way". Applied to funk guitar, this means leaving a LOT of space, without playing muted strums, etc. Give a listen to the following mp3 clips:
James Brown - Sex Machine mp3
Notice the guitar player is playing NO muted strums in this part - simply repeating a four strum figure. Many of us, when playing a part like this, would feel a natural desire to include muted 16th note strums within the part. Avoid doing this.
The Meters - Just Kissed My Baby mp3
The guitar plays a single-note line, but the minimal guitar part is very disciplined in that it does not stray from the riff.
The JB's - Pa-arty mp3
This song sounds "busier", and there are two guitarists, but listen to each of them, and you'll note they're repeating the exact same parts again and again, with no variation. Another example of the need for discipline in funk music. Pay attention to all instruments here - everyone plays their specific part, which adds to the whole.
"Busy" Funk
This approach is a little different - perhaps a little less disciplined than the above style of playing funk. There is less space in this style of music, and guitar players in this style tend to play a lot more muted string strums, etc. The result is a groove that usually feels a little less laid-back, and more "frantic". Have a listen to a few songs in this style:
Tower of Power - What is Hip? mp3
Really active bass and drums give this song it's somewhat frenzied, albeit very funky sound. The guitar player wisely stays largely out of the way, keeping muted strumming to a minimum (too many musicians being too busy at once can yield disasterous results).
Stevie Ray Vaughan - Superstition mp3
SRV's take on the Stevie Wonder classic is a great example of this style of funk music. Vaughan fills up the space in the music with muted string strums to propel the music forward.
Graham Central Station - The Jam mp3
Bassist Larry Graham leads this one, and it's another example of very robust, in-your-face funk, with little left to the imagination. Lots of busy strumming by the guitar player.

