Even today, in the course of a "puja" or ritual worship, the devotee, using a Sanskrit phrase, says, "nAnA vida parimaLa pathra pushpANi samarpayAmi" (I offer many types of fragrant leaves and flowers). The offering of fragrant leaves (such as thulasi) seems to be far less than the offering of flowers.
Over a period, certain flowers have, indeed, come to be associated with certain gods and goddesses in the Hindu religion (I don't know if this is true of other religions as well.) The Hibiscus, for example, is special to Lakshmi in several of her forms, and to the Sun God, Surya. Hanuman is believed to reside in the roots of the pArijAtha tree. Fragrant blossomes, of course, are universally beloved of the gods,and indeed, a flower like the lotus is completely inseparable from the Hindu religion, philosophy and iconography!
There are sometimes exceptions..the thAzham poo, or Screwpine flower, for example, is never offered in worship to Shiva, and there is a nice little story (as always!) to account for it.
Once, Shiva stood in the form of an eternal and endless flame, and Brahma and Vishnu, to settle an argument (the gods are always having arguments about who is the greater...they are very human!), they decided to see which one of them could find one extremity of the flame. Vishnu took the form of a boar and dug deep into the earth, and Brahma, in the shape of a swan, flew up into the heavens to find the top of the flame. As Brahma started tiring of the upward ascent, he found a screwpine flower falling from Shiva's locks, and asked the flower to bear false witness that Brahma had, indeed, found the top of the flame, and got the flower as evidence. Shiva, of course, knew that Brahma was lying, and cursed him never to have temples to him (there are still very few temples to Brahma) and cursed the flower that it would never more grace His locks. Er, mythology does not say that therefore, Vishnu was the greater!
I am unable to decide whether it is the aesthetic appearance of multi-coloured flowers that appeals to one's sense of devotion, or whether, over centuries, one is culturally conditioned to love the sight of flowers in a shrine. Either way, one cannot see a church, temple or gurudwara which is not bedecked with flowers.
In churches,very often, flowers are arranged in water, but everywhere else, it is flowers that are plucked, and sometimes woven into a garland, that are used. Surely, having wilting and dying flowers is not a great way to offer devotion? I ask this question rationally, but culturally and emotionally, I too derive great satisfaction from decorating my own home puja with flowers.
I suppose I will never be able to find out more about the origins of the use of blooms in religious worship, as it is heretical to too many people to think of worship without them.
But...if any of you have any information or ideas....share them please!