From a recent ad for Oceana, a non-profit, here's evidence that it really matters whether you emphasize your desire to work at a place:
The Office Coordinator will support the Vice President of Global Development and will assist in fundraising efforts of Oceana. Oceana will only consider an individual who has a clear passion and interest in the oceans and marine conservation. (see www.stopdodo.com for more detail on job.)
I sometimes see this stated, and believe it is implicit in every single job posting: employers want to hire the person who really wants to work specifically for them. This goes for both non-profit and for-profit organizations. Just because they may not have a "feel good" mission like a non-profit, don't think for a minute that for-profit companies are exempt from wanting to hire "true believers." Just like non-profits, for-profits want to hire someone who cares enough to learn about their company, industry, and business model. When you demonstrate your knowledge and enthusiasm for a company or organization, you demonstrate how you will be on the job - eager to learn and enthusiastic about your work. As T. Harv Eker says, "how you do anything is how you do everything." This applies especially in job seeking.
If you don't care about a cause now, is there a chance you would care later? It's OK not to know if you care about an organization, mission, industry, or business purpose - as long as you put in the effort to find out if you do. So go ahead and find out quickly. Do a little research:
* read the company website
* go to Wikipedia to find out more about the topic
* do a search on the organization to see what press they get and what others say about them
* ask your friends what they know and think
* do a "gut check" to see if you have even the flickering of concern, enthusiasm or passion
You may find that you really DO care about the cause in which case use that enthusiasm in your cover letter. You can even be more enthusiastic in your letter than you actually feel, as long as you authentically care to some extent. Passion for a cause often grows over time.
Or you may find that you don't care, so you can cross that job off your list. Don't waste your own or the employer's time.