You must done a lot of business to figure out all this on your own. The problem is, your intuition is just plain wrong! Here're facts from Producer Kouji Taguchi, whose C.V. includes a little show by the name of Full Metal Alchemist:

The publishing companies have to foot the production, marketing, and advertising costs in order to put anime on television. One episode would cost 10 million to 20 million yen (about US$110,000 to US$220,000) to produce. In addition, the publishers have to pay the sponsoring fee for the timeslot, which can cost about 50 million yen (US$560,000) for late-night timeslots on five to seven stations for two cours (six months). However, sponsoring timeslots on UHF stations cost about half of that. The total budget for an anime series on the level of Fullmetal Alchemist (which aired on key stations for one year at 6:00 p.m. on Saturdays) was at least 500 million yen (US$5.6 million).

Taguchi added that it is simple to see how publishers profit from broadcasting television anime. For example, each compiled book of the Fullmetal Alchemist manga costs buyers 420 yen (US$4.70), but once author's fees, printing costs, and paper costs are subtracted, publishers are left with 150 yen (US$1.70) per book. If it takes at least 500 million yen to fund a television anime, the anime has to boost the total manga sales by at least 3.3 million copies to be profitable for the publisher.

Taguchi estimates that a total of 4.6 million more Fullmetal Alchemist manga volumes were sold thanks to anime.... Saki anime... the average rose to 350,000 afterwards... Kuroshitsuji volume... total sales reached 910,000 by the end of the anime

http://www.animenewsnetwork.com/news/2009-10-09/producer/no-square-enix-anime-lost-money-in-8-years

Plenty of "folk knowledge" circulating among the English anime fandom. Some of them are indeed wrong, but you don't bust those bubbles via intuition or just guessing at the answers. If you feel something's off, check the facts first.