Seals get good publicity because they are "cute". They have faces that apparently communicate innocence and softness to some people. That makes it less popular than shooting wild boar or killing off overpopulations of deer or bears, example.
http://www.dfg.ca.gov/hunting/bear/mgmtharv.html
The population is managed and has still been allowed to grow : "A 2004 harp seal population survey found the harp seal population to be stable and healthy at approximately 5.8 million animals, nearly triple what it was in the 1970s."
History and information:
http://www.dfo-mpo.gc.ca/seal-phoque...faits_tl_e.htm
Most people couldn't stand to see how cattle are turned into steaks either... but that is life.
Alex