Web Site Building

It all depends. If you are going to be responsible for administration of the web server, and you have experience in Linux, then you would undoubtedly know that you want to use Apache. If you do not have experience in Linux and do so in MS, then you can use 2003 server with IIS. As long as you lock down the server and place it behind a properly configured firewall you would not need to pay mind to every security bulletin.
If you are going the MS route then you may as well use FrontPage to create the pages themselves. Alternately you can use Dream Weaver. If you want to use ASP as opposed to HTM* though you will need to use MS as Apache does not natively support ASP. On another token, if cost is a factor then obviously Linux and Apache is a more suitable scenario.

Building a website for a non-profit is a challenge. They can't afford much, and a full-time admin is never in the budget. Also, most ISPs will not allow customers to host their own sites. For these reasons, I recommend that you purchase space from a hosting service, rather than build a web server. Many hosting services offer online site-building tools, which can save you a bunch on development tools. They also usually offer a number of templates for you to use and customize. Being artistically challenged myself I find that attractive.

That being said, I develop websites at home on a Win2K server using VisualInterDev from Microsoft. It's not an easy tool to use, but it's fairly handy once you learn it. FrontPage does a decent job, and I hear the new 2003 version is much better. Most of my work these days is using Active Server Pages, or ASP, and a great book for creating ASP sites is Beginning Active Server Pages 3.0 by Wrox Press. ASP.Net is starting to catch on, though hosting services still tend to charge extra to support it. But Microsoft offers a free development tool called WebMatrix if you'd like to try it out. Search http://msdn.microsoft.com for details.

Personally I would reccomend you try another option. More specifically, contracting a 3rd party host. I personally love 1and1 hosting. There website is http://www.1and1.com

they have great prices! well within anyones budget.

hope that helps.
best of luck