Pharmacology is still a relatively young science. In the good old days of drug development, there would inevitably be side effects for most drugs that we take, as they will act on other tissues and organs, other than the intended targets.
For more specific targeting of the cells, using the virus offers an effective tool. One group managed to develop a liposome-based vector whereby the liposome was decorated with viral envelope fusion proteins (Kaneda, 1998). Developing viral nanoparticles as a vehicle to deliver drugs is also another development in progress.
After all, it's using the scourge of mankind as a delivery vehicle of therapeutic agents to specifically target cells of interest whilst leaving the rest alone. Specific drug delivery will eventually lead to fewer side effects.
Citations
1) Kaneda, Y. Fusigenic sendai-virus liposomes : a novel hybrid type liposome for gene therapy. Gene therapy 1998, vol. 14, no 5, pp. 387-572 (2 p.3/4), pp. 553-572.
2) Virus Nanoparticles Provide Convenient Oral Drug Delivery Vehicle. http://nano.cancer.gov/news_center/nanotech_news_2005-10-10a.asp
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