"Back when software was sold prepackaged in retail stores"
Comparing apples to oranges? Physically packaged software had inherently higher costs (and good manuals) - warehouse stocks and shelf space, more intermediaries, unsold obsoleted products, etc. - you do exactly expect downloadable software to be far cheaper.
Also, remember anti-trust laws are also against cartels and dominant positions, not pure "monopolies" only. Let's see what the court will rule.