Besides losing habitat where they overwinter in Mexico and where they live in the U.S. in the spring and summer, the use of Roundup-Ready crops has killed many, many milkweed plants that they used to lay their eggs on, because milkweed cannot survive being sprayed with the Roundup herbicide like the genetically-modified corn and soybean can.
http://www.nytimes.com/2013/11/24/sunday-review/the-year-the-monarch-didnt-appear.html?_r=1&
However, there is some hopeful news. Good job, American public, though I wish more of you were willing to plant milkweed.
"By extrapolating numbers to the entire country, the authors estimate that Americans would pay $933 million and $473 million for nectar and milkweed plants, respectively."
Because monarchs are so charismatic and well-loved by Americans, who have fond memories of seeing them in great numbers when they grew up, or raising their caterpillars at home or in the classroom, Americans are willing to donate to monarch conservation. Maybe we can get some good things going.
http://conservationmagazine.org/2013/10/people-willing-shell-money-monarchs/
You can read the scientific article the link is writing about here:
http://onlinelibrary.wiley.com/doi/10.1111/conl.12065/full
Also, if anyone has any monarch questions for me, feel free to add a comment and I will do my best to answer them!