One reason why big O gets used so much is kind of because it gets used so much. A lot of people see the notation and think they know what it means, then use it (wrongly) themselves. This happens a lot with programmers whose formal education only went so far - I was once guilty myself.
Another is because it's easier to type a big O on most non-Greek keyboards than a big theta.
But I think a lot is because of a kind of paranoia. I worked in defence-related programming for a bit (and knew very little about algorithm analysis at the time). In that scenario, the worst case performance is always what people are interested in, because that worst case might just happen at the wrong time. It doesn't matter if the actually probability of that happening is e.g. far less than the probability of all members of a ships crew suffering a sudden fluke heart attack at the same moment - it could still happen.
Though of course a lot of algorithms have their worst case in very common circumstances - the classic example being inserting in-order into a binary tree to get what's effectively a singly-linked list. A "real" assessment of average performance needs to take into account the relative frequency of different kinds of input.
