It seems as though a lot of anime go through a production cycle where they put out a series that seems fairly popular, but ends long before the manga's storyline does. Obviously, a big reason for making anime is to get people to buy the original manga, but if the anime series itself were turning a profit it's tough to imagine (from my American viewpoint, anyway) that the producers would abandon it, when it could easily continue (given its proven popularity, voice actors lined up, storyline set, etc.)
Is there an overarching reason? Do many anime not turn a profit?
Obviously this is a fairly blanket statement and is hard to qualify because of secrecies in company financials, but I think it's reasonable to assert.
I also realise I'm not directly answering your question about dropped manga adaptions, but addressing the question broadly. I think most points probably apply to that situation also, but these are some of the reasons in general why anime fail/return losses:
Anime as a loss-leader
Anime is often used by companies as a promotional tool for their other merchandise. This is often the case with children's mecha shows - They will watch the show on TV and then potentially buy the DVDs, toys, albums, etc. As an interesting side note, since about 1990 children are more likely to buy hero toys than villain toys - hence several combining mecha shows.
Another example as to how shows act as advertisements is low cost harem anime. Whilst not immediately as obviously merchantable as a show like Gundam or Power Rangers, The large female cast that the protaganist has to choose from has the potential to have their own figurines, body pillows, etc.
These mean that anime doesn't have to turn a massive profit (or indeed a profit at all) - that's up to the sales that it inspires.
The evolution of anime itself is deeply associated with advertisement, even since its inception when it was used solely for advertisement rather than as a standalone medium. In Hayao Miyakazi's biography "Starting Point" he mentions that one company in particular was known to contribute a third of their target anime's total cost (Note that this was at an earlier point in history). This amount would typically be around 90% of a successful toy company's advertising budget.
There's a stereotype of otaku in Japan that they buy 3 copies of any one DVD/Book - "one to read, one to collect, one to lend". The consumers of anime in Japan, whether children (A good market worldwide) or otaku are very keen on merchandise and spending on a franchise. It is the combined revenue streams that the anime creates, combined with the show itself which usually lifts the show into profit.
This is the main reason why an anime would be turning a loss.
Relying too heavily on emulating success stories
This is a big one too. Once a very successful show hits the market (for example Evangellion, Akira, K-On!!, Pokémon) many clones will follow.
The same phenomenom can be see in bookstores - The amount of romance vampire books in stores went from 0 -> many after Twilight's success. Similarly 50 Shades of Grey did the same for erotic romance for women.
There is only so much capacity in the market for cloned shows, and more than likely none of them will be as successful as the original. This often leads to a situation with a few big winners and many losers.
Too many blockbusters
The ideal time to release your amazing anime series is to pick the season that has the highest viewing rate of your target audience. Hence, shows that target the same audience may be heatedly vying for the same audiences attention. Usually one show will win, and the others will lose by a sizeable margin.
There have been several media studies that have shown that usually only one film/series occupies a viewers fanaticism at one time period. This is what has lead to the yearly blockbuster summer and Christmas successes in Hollywood.
Things go wrong, often
When you are still animating episodes whilst the first ones are airing, any delays can set the whole show back. What usually happens is that recap episodes are shown, animation quality drops in the latter episodes and potential postponements of episodes in the worst of cases. These things transfer to the quality of the production and hence affect the impressions on viewers, which then affect sales, and so forth.
This kind of fits into the previous item, but when budgets are tight (which they usually are for anime) studios cannot afford to replace sick animators, redo scenes that don't fit well, etc. Another problem with tight budgets is that studios often have to outsource animation to cheaper countries like China - which in itself has problems of communication issues.
Anime that are received well in their first season often announce another, or several new seasons. The problem with this is that each season the audience dwindles - Viewers become less and less likely to stick with a show as the time investment increases. It's a difficult call to make for the directors to stop the broadcasts before the series starts to become loss-making.
And just as a final note, I don't believe there is one over-arching reason. Each studio is different, has different priorities, objectives, revenue streams, etc.
Anime is much bigger in Japan. There are lots of mangas that were given a shot at anime adaptation, but they didn't get a following and eventually got pulled. In my opinion, the manga has to be popular in Japan first before the network heads start to export the anime officially.
There are other reasons aside from profit. Take Gintama for example; I can't be sure if they were pulled off air because of profit (which I doubt) or because the network wasn't happy with the show's direction.
So, yes, the big reason why they get pulled off air is because the anime didn't make enough profit. It's a competitive market.
Note it doesn't need to produce losses: it just needs to produce less than alternative.
Studios have limited resources: they often can produce maybe two series in parallel, sometimes not even that. Expanding on that is costly, and may well bring serious losses if all "pipelines" aren't filled with profit-generating products.
So, if the managers notice a new, promising series - obtained a sure-fire scenario, and a different one is nearing end of season 2, with dwindling audience, they must decide what to produce: season 3 of the old thing, which will almost certainly produce less cash than season 2, following the dwindling trend, or maybe the new and revolutionary thing for which TV networks have already lined up, and earn much more. Or, potentially, hope that hiring a bunch of animators and getting them a new studio with equipment will cost less than combined profits of the two shows. Which it rather won't.
You have to remember that it's far cheaper and easier to produce a manga than it is to produce an anime -- it takes fewer people to produce a manga, which means less money is needed to pay for production, even if you pay everyone involved a huge salary (and you usually don't).
More investment means more risk, so if an anime doesn't turn a big enough profit fast enough, it may not warrant further investment.
You can keep a crap manga going a lot longer than a crap anime, if only because the bar for financial security is that much lower.