Fundamentally, a canyon is usually water carved, meaning that their is often a source somewhere in it. This is the foundation for most of its life, because, unlike most of the desert, there's a readily available source of moisture. Much like an oasis, this gives rise to ample vegetation, which in turn gives rise to animal life.
Canyons vary greatly in appearance and vegetation, since they're derived from differing bedrocks, ecologies and orientations. It is entirely possible that plants found in one canyon are not found in any other, or are only found in a small number of them. Ultimately, this diversity is one of the reasons that canyons are so precious.
There are, however, some significant threats to canyons in the desert, most of which are derived from a human source. One is the use of canyons for recreation. Normally, this is not an issue, but there are members of the public that do not treat the land with the respect that it deserves. Some use the canyons as a garbage dump, leaving their waste behind instead of taking it to a proper disposal site. More sinister is the presence of off
highway vehicle riders. While many of these riders are not actively malicious, there is a significant number that are of the mindset that they can willfully ignore the designated ares where they can ride, and bushwhack through any part of the desert, including the canyons, that they want. The amount of damage that they can inflict with this activity is significant, and each time, it compounds the problem, as new routes are formed, which encourages new riders to take the illegal passage.
The other threat is not to the vegetation directly, but to the source of their life: water. As human growth continues unchecked, we must find new sources of water. And in finding those water sources, we often steamroll natural areas in the process. If the water supply in a canyon is lost, or even reduced, it can have a dramatic effect on the ecology. Fortunately, most of the canyons are not being actively tapped, or are only used for small wells. However, if a larger municipality began to use the water, then it could seriously effect the canyons' health.