How to stop auto refresh?

As far as I know there is no auto-refresh setting in Safari.

Do you have any third party add-ons installed?

Sorry, then I completely fail to understand your original question:

How can I disable auto refresh in Safari 4.0.4?
Auto refresh is very annoying when you are reading a page...

How can you disable, or even see, something that isn't there?

Or is it a script in The New York Times HTML page?

Yes - probably a Javascript.

http://en.wikipedia.org/wiki/Meta_refresh
The page is controlled by the authors and there is nothing a viewer can do to change it.

Yeah I guess, without quickly hitting the button that says 'loading' at the right hand side of the address bar (Which is what I end up doing sometimes).

Some people just pretend they don't understand eh Evita? I also find this auto refresh very annoying. Everytime when I'm watching some video on my favourite news webiste, it stops half way and refreshes itself, forcing me to restart the video. It is cool on the other hand that you are sure you have the latest news ever! lol
The solid blogger website says the following:

"You can find several websites with <meta http-equiv=”refresh”> HTML tag inside their source code. This code is used to reload web pages automatically in regular intervals and this command works with almost every browser like Internet Explorer, Firefox, Chrome, Safari and Opera. Webmasters add this code to increase their website page views count and lower their rank in Alexa. However, this is very annoying since the page reloads automatically and you don’t get a chance to read it’s contents without interruption."

And according to them, the solution for our problem is using Firefox where fortunately they have the option to stop the auto refresh. Take a look at the instructions they give:
http://www.solidblogger.com/disable-auto-refresh-web-pages-in-firefox/

Cheers.