If I understand your question, you are asking why weeds and not domesticated crops develop natural resistance to herbicides. That’s an interesting question.
In order to answer your question, I think it is important to understand some concepts about weeds and domesticated crops. Weeds typically produce a large number of seeds per plant, have high genetic diversity, long seed dormancy and high seed dispersal (see http://extension.psu.edu/pests/ipm/schools-childcare/schools/educators/curriculum/weeds/introweeds). These traits allow weeds to persist in the environment and in particular high genetic diversity enables the weeds to adapt to various environmental and human selection pressures.
On the other hand, crop plants have been domesticated to remove many of these same traits. For a domesticated crop variety to be successful in the marketplace, it needs to be genetically uniform within the variety so it can be grown effectively in our highly managed cropping systems, have a high seed germination rate (not high seed dormancy) and hold the seed on the plant so that it can be harvested and used. These differences between weeds and crops make it much more likely that the weeds can adapt to selection pressure than crops. Since herbicides place a strong selection pressure on the weed population, only when a resistant type occurs does it survive, reproduce and increase in number. In contrast, herbicides are only used in a crop when it is safe for that crop – otherwise the crop is damaged or killed. Thus, there would be little selection pressure to develop herbicide resistance.
There has been a great deal of discussion lately about the use of herbicides in agriculture. History shows the use of compounds which inhibit the growth of plants [herbicide] for over 100 years.1 Weeds (loosely defined as any plant growing where it is not wanted) consume soil nutrients, water and can block sunlight from crops. Along with physical control mechanisms like plowing farmers use herbicides to help reduce yield loss from ‘weeds’.
Weeds have developed resistance to almost every form of control. The development of herbicide resistance is almost as old as herbicide use. According to weedscience.com, "There are currently 396 unique cases (species x site of action) of herbicide resistant weeds globally, with 210 species (123 dicots and 87 monocots). Weeds have evolved resistance to 21 of the 25 known herbicide sites of action and to 148 different herbicides. Herbicide resistant weeds have been reported in 63 crops in 61 countries." 2
GE crops were first commercialized in the mid-1990s so it is clear herbicide resistance predates GE crops and is not unique to this technology. Having said that it is also clear that over reliance on one particular herbicide has contributed to the rise of resistance to that herbicide. Better stewardship must be the hallmark of future agriculture if they want to continue to have effect herbicides. Rotation of other herbicides, cover crops and other practices must be used to manage the inevitable development of resistance to particular herbicides.
The most common herbicide associated with GE crops is glyphosate. It targets an enzyme system that exists in plants and microbes but not higher animals. This helps give selectivity and therefore reduced environmental impact to non-target species. The effectiveness of this compound has also allowed for large reductions in other herbicides that often had much higher environmental impacts.
All agriculture has impact on the environment, there is no free lunch. The trick is to find farming practices that give maximum yields with minimum impacts. GE crops and in particular herbicide tolerant crops have contributed to this goal. Increases in herbicide tolerant GE crops have allowed farmers to greatly reduce of in some cases eliminate plowing of the soil. This results in increased organic content of the soil, reduced soil erosion and ground water contamination. All are improvements the average person is largely unaware of with respect to GE crops. This is also why farmers, when given the choice, have overwhelmingly adopted this technology to help them produce more food with less environmental impact.
In the coming decades we must use the best of every agricultural technology including herbicide resistant crops if we are to feed 9-10 billion people on the same of less land more sustainably.
1. A History of Weed Control in the United States and Canada http://www.jstor.org/stable/pdf/4041862.pdf