The reason that print+web packages don't cost significantly more than web-only is because print advertising is still a lucrative business. NYT can a a absolutely justify giving away the paper to subscribers on that basis.
Except, if that were true, why not just make it a free paper? Presumably ad targeting... I understand the limitations of their existing revenue model. It just results in some pretty consumer-unfriendly offerings, at the expense of readership and penetration...
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EDIT: Went back to look at the numbers... They have tons of online eyeballs - those eyeballs just don't make much money. They manage to double their digital revenue with the paywall. Even so, it's dwarfed by the print revenue.
This may shift as advertisers see the value of targeted online user groups... I could totally imagine the NYT of the future being a collection of blogs dealing in Tech, Biz, World News, Local News, etc. Ads on the Biz site would be targeted differently than on the World News site. This might give advertisers what they want in terms of a differentiated audience.
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From the 2014 Annual Report:
Average Paper Circulation in U.S. (Int'l)
648,900 (219,500) for weekday (Monday to Friday)
1,185,400 (220,500) for Sunday
Paid Digital Subscribers
910,000 as of December 28, 2014
Monthly (Annual) Digital Readership
31MM (372MM) unique desktop/laptop visitors (U.S.)
42MM (504MM) unique desktop/laptop visitors (WW)
28MM (336MM) unique mobile device visitors (U.S.)
Off these eyeballs, they made:
$667.5MM from print subscribers
$169.3MM from digital subscribers
$483.5MM from print advertising
$178.8MM from digital advertising