What seems to be surprising is that owl is considered inauspicious even though it is the vehicle of goddess Laxmi (goddess of prosperity).
Not only in India, but even in some other countries, owl is considered inauspicious. For example, some people in Europe in South Africa believe that hooting of an owl portends incoming death. There is nothing surprising in that because they do not have any concept of owl being the vehicle of the goddess of wealth. There are also some cultures, where owl is believed to bring good luck.
In Hinduism, there is belief that owl is the vehicle of goddess Laxmi. So, the question is why Hindus consider hooting of an owl as inauspicious?
Bengalis are foremost in worshipping goddess Laxmi. It may surprise you, but Bengalis believe that the hooting of an owl is a good sign and it brings wealth and happiness. But many other Hindus (esp. in North India) consider the hooting of an owl as bad omen. There are two reasons for this. One is that the carrier of goddess Laxmi is white owl while the owls that we normally see is dark coloured. Another reason is that the voice of an owl is frightening and is therefore associated with the sound of witches.