Because out of control transposable elements are a major danger, cells (ours and those of most other organisms) have an elaborate maximum-security system for shutting these bad boys down. Just how this lockdown system works is an active area of research, and a recent paper revealed how plant cells enforce security and prevent prison breaks by these DNA parasites.
The risk transposable elements pose to us is probably minor because we're made up of many, many cells, and a transposon-induced mutation in one of those cells generally isn't a big deal. But the harm to our future offspring posed by parasites going wild in our germ cells (i.e., sperm and egg cells) is huge - a harmful mutation in a germ cell means harmful mutations in all of the cells of the embryo produced from that germ cell. If there were absolutely no control over transposable elements in germ cells, the resulting mutation rate would probably be higher than our species (or just about any multi-cellular species) could tolerate.
Both plants and animals use a system of DNA modification to silence transposable elements in our genome. Enzymes add chemical tags, called methyl groups, to the DNA, and these tags are a signal for gene silencing - regions of tagged DNA are wrapped up tightly and prevented from being transcribed into RNA. (Transposable elements have to be transcribed in order to replicate themselves throughout the genome.) In other words, DNA methylation is part of the straightjacket that keeps harmful DNA shut down. (DNA methylation isn't only for transposable elements - other genes also get silenced by methylation, but the reason why is not always clear, although some of these genes are de-methylated in various cancers.)
The problem with this methylation straightjacket is that it wears out over time. This problem becomes especially acute when it's time to pass DNA on to the next generation - how does a cell restore missing methylation tags when they wear out?
A group of researchers working in France and Spain set out to find out how the DNA methylating enzymes find their way through the vast territory of the genome to those hazardous, transposable element-containing regions that need to have their chemical tags maintained.
Previously, scientists had thought that DNA methylation in plants, once it has been severely compromised, could not be restored, because once a plant genome sustains a major loss in methylation (caused by a mutation in a methylating enzyme), that loss persists across multiple generations.
On the other hand, in normal plants, methylation is incredibly stable over generations, in spite of the fact that the actual chemical tag can be, over time, spontaneously lost. Thus, the researchers reasoned, there has to be some sort of mechanism maintaining the integrity of the methylation security system.
It turns out that there is a system in plants to restore lost methyl tags. This system is based on another classic defense mechanism against transposable elements, called RNAi. What happens is that short RNA molecules, produced during the process of RNAi, and which hone in on specific stretches of DNA, act as guides for the methylating machinery, keeping parasite-infested areas locked down.
The bottom line is this: our genomes, and those of most other organisms, are full of hazards that need to be controlled by fail-safe procedures. The molecular machinery that locks down dangerous regions of the genome is constantly patrolling our DNA to protect us from ourselves.