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If the site is written in a standard programming language, shouldn't all browsers work equally well??
The problem is that these sites you come across are *not* developed using standard-compliant languages. They are developed and served; and meant to be viewed, using Microsoft technologies.
... So when we take into account the fact that IE is *not* compliant with a lot of international standards, and add to that the Microsoft development/ server/ browser proprietary-ness, you end up with lock-in, where users are forced to use Microsoft technologies.
I develop most sites using what is commonly referred to as a LAMP stack - a Linux-based server, with the Apache web server, the MySQL database and the PHP scripting language. These are all open source, free technologies that conform to standards and are consistent across all major browsers. A MS-trained developer, however, may be using all MS: The Windows OS with the IIS web server, a MSSQL database and the ASP scripting language. This latter work flow makes it much easier - almost encourages the developer - to craft sites that work with IE only in some manner. My wife employer - The local school board, uses this model; and we, without a Windows system in the house, have a bugger of a time sometimes using the employee portal.
[This is gross over simplification] I think the market share between LAMP and Windows-based servers globally is *about* 60-40, but the trend is favoring MS:
http://news.netcraft.com/archives/2008/09/30/september_2008_web_server_survey.html (2nd graph from the top).