This report is quoted in: McCafferty, P. (2008). Bloody rain again! Red rain
and meteors in history and myth. International Journal of Astrobiology, 7, 9-15
(@rchive.is) , and was the first reportage of the Govt of Indian's analysis of
Kerala rains posted here by way of one of its scientists whom I contacted.
My full red-rain report is in : Noesis, Mar 2006, p 10-18.
Possible Causal Mechanism
of Kerala's Red Rain
(c) 03/22/06 Ian Williams Goddard
Imagine stepping out into a rain shower only to find it was raining blood! That's what it looked like to residents of Kerala, India in 2001 when red rains fell in scattered areas over three months. Some rains were even yellow, green, or black.  Experts scrambling for answers first suggested that fallout from a hypothetical meteor explosion may have colored the rain. More recently, news reports suggest such a meteor burst may have colored the rain with extraterrestrial cells. [2-4]
Research Overlooked by the Media
Overlooked by recent news reports is the study commissioned by the Government of India in 2001, conducted by Sampath et al. They found that the rainwater was colored by spores from a locally prolific aerial algae of the Trentepohlia genus.  Accounting for all the observed colors, Trentepohlia spores can be red or green, and degrees of their dilution can make rainwater appear yellow or black. Sampath et al. estimated that at least one ton of the spores fell in the rain  and they cited the still-unanswered question: How did so many local spores contaminate the rain, and why in only scattered areas during the 2001 monsoon? 
Regarding the extraterrestrial-microbe hypothesis, Sampath et al found no meteor debris in the colored rainwater. Moreover, the extraterrestrial hypothesis rests on the assumption that a loud thunder and flash of light during a storm was an exploding meteor. However, a better causal explanation for a thunderous sound and flash of light during a storm is thunder. Additionally, just the fact that the colored rains fell sporadically over three months refutes a meteor-burst event as the cause. Finally, given that the spores grew in culture into a known species of algae, the extraterrestrial hypothesis seems to be without factual grounding.
An Answer to the Mystery?
But the question remains: how did so many local spores contaminate rains in scattered areas? While rains colored red by desert sands or yellow by pollen have been reported and analyzed around the world over several centuries, [7-12] the Keralan rains may be the only cases of rain colored exclusively by spores. So what might cause such a proliferation of spores? Unique rain patterns in Kerala during 2001 may have played a role. Given a period of above-average rainfall weeks before and then below-average rainfall just prior to and during the colored rains,  there may have been an algae bloom and then a build-up of spores.
So a simple explanation would be that the winds of a storm lofted up spores that accumulated during the dry spell and then its rains washed them down. However, most airborne spores of the given ultra-light size (3 to 5 micrometers ) would be swept aside by falling raindrops rather than being absorbed into them.  Yet raindrops in Kerala were so thoroughly contaminated by spores that in some cases they were as red as blood. The rain was also reported to have been clear for some time prior to the sudden onset of colored rain. 
Those facts do not favor a simple washout but suggest instead that spores had already contaminated some portion of the rain before it fell from the clouds, which in turn suggests the transport of local spores into local clouds followed by their local rainout. Such a local model differs from the atmospheric dynamics underlying typical colored rains where a potpourri of aerosols are transported from remote locations via upper-atmospheric winds. So by precisely what mechanism could such local aerosol input and output occur?
The anatomy of a self-propagating storm provides an attractive causal model.  Such anatomy is depicted in the following illustration showing by way of arrows the possible paths that might be taken by accumulated spores lofted up by the warm updraft flowing from ground-level forward of a storm up and into the storm.
It is useful to think of such a storm as a machine that inputs airborne spores, processes them into rain droplets by absorption or nucleation, and then outputs spore-colored rain. Given the variable proclivities of machines or of the input thereto, it could happen on rare occasion that the output is atypically concentrated. In this case such atypical output may have been due to an atypical input of built up local spores. Furthermore, given the likelihood of scattered showers due to below-average rainfall within the timeframe of the colored rains, such concentrated spore-rain output might be expected to occur only over scattered areas as reported.
Therefore, the storm-circulation model provides a possible answer the question raised by Sampath et al: How did so many local spores contaminate the rain, and why in only scattered areas during the 2001 monsoon? An unusual pre-monsoon wet period spurred an algae bloom; then spores accumulated during a dry spell; then the spores were lofted up and drawn into scattered storms wherein they were concentrated and then rained out onto scattered areas. Of course the final answer can only come from further research of the Keralan environment.
For detailed analyses of a range of possible causal mechanisms of the Keralan red rains, see my full paper: Goddard, I.W. (2006). The Colored Rains of Kerala: An Exploration of Possible Causal Mechanisms. Noesis, 180 (March): 10-18.
 Mathew, R. (2001). Multicolour rain. The Hindu, Jul 29. (@rchive.org)
 Editors. (2006). Skepticism greets claim of possible alien microbes. World Science, Jan 5.
 Gentleman, A., & McKie, R. (2006). Red rain could prove that aliens have landed. The Guardian, Mar 5. (@chive.org)
 Muir, H. (2006). When aliens rained over India. New Scientist, Mar 2.
 Sampath, S., Abraham, T.K., Sasi Kumar, V., & Mohanan, C.N. (2001). Coloured Rain: A Report on the Phenomenon. CESS-PR-114-2001, Center for Earth Science Studies and Tropical Botanic Garden and Research Institute.
And reported in: Indian National Report for the International Union of Geodesy and Geophysics 23rd General Assembly, July 2003. Indian National Science Academy. See pages 31-2.
 Kumar, V.S., Sampath, S., Mohanan, C.N., & Abraham, T. K. (2002). Colored rain falls in Kerala, India. Eos, Transactions of the American Geophysical Union, 83(31), 335.
 Thompson, D.P. (1849). Introduction to Meteorology. London: William Blackwood and Sons, 150-66.
 The editors. (1851). On the Infusoria and other Microscopic forms in Dust-showers and Blood-rain. The American Journal of Science and Arts, Second Series, 6, May, 372-83.
 McAtee, Waldo I. (1917). Showers of Organic Matter. Monthly Weather Review, 45(5), May, 217-224.
 The editors. (1968). Red Rain. Nature, 219, 112.
 Associated Press. (2006). Storm drops dark brown snow on Colo. Feb 17.
 MosNews. (2006) Creamy pink snow covers Russian region. Mar 13.
 Kumar, R.K. & Revadekar, J.V. (2001). Weekly evolution of the 2001 Indian summer monsoon season. Indian Institute of Tropical Meteorology.
 McDonald, J.E. (1962). Collection and washout of airborne pollens by raindrops. Science, New Series, 135(3502), 435-6.
 Scorer, R.S. (1978). Environmental Aerodynamics. New York: John Wiley & Sons, 430-3. And in: Scorer, R.S. (1997). Dynamics of Meteorology and Climate. New York: John Wiley & Sons, 519-21.