Ok, currently there's 4 major options for browser based games.

Java - Revived mostly due to Minecraft and Android, Java requires a plugin with about 75% market penetration (source). It's also a fairly complicated language that really isn't suited for first time programmers. There's advantages to using it, but it's probably not the best option.

Unity - Great browser plugin for developing 3d games, tons of tutorials, and support for C#, Javascript, and their own scripting language. However, the more advanced features require paying for the pro version (~$1,000), and it's not really suited to a team development environment (unless you pay for the pro version...). It also doesn't really handle 2d games very well, though it can do 2d if needed.

Flash - Market Penetration is about 95%, and a large amount of people are using Flash for their games, it's great for 2d, has recently added support for 3d, and has toolsets and libraries out there to make development quick and easy (Flashpunk and Flixel). That said, networking could be a problem (I don't know how performance is on real time networking...), and it only really supports left click (right click is massively useful for an RTS) Flash is becoming more useful for games, but most of these games are single player with high score tables, or similar sorts of things. Very few mobile devices support Flash, as well.

Javascript/HTML5 - The biggest issue here is that support for HTML5 is not yet 100%. You're effectively cutting out anyone who uses Internet Explorer, or older versions of other browsers. Performance is also a fairly major bottleneck, since Javascript is a bit slower than Flash or Unity plugins. Additionally, even though Javascript can be pretty easy to learn, there are a few minor/major problems with it that can cause new programmers confusion. The trick here is to find a tool or library that can help development. You can probably find some info here: http://html5games.com/

Side note: there's other options out there, but most of them have even less support or market penetration than anything listed here.

Ok, currently there's 4 major options for browser based games.

Java - Revived mostly due to Minecraft and Android, Java requires a plugin with about 75% market penetration (source). It's also a fairly complicated language that really isn't suited for first time programmers. There's advantages to using it, but it's probably not the best option.

Unity - Great browser plugin for developing 3d games, tons of tutorials, and support for C#, Javascript, and their own scripting language. However, the more advanced features require paying for the pro version (~$1,000), and it's not really suited to a team development environment (unless you pay for the pro version...). It also doesn't really handle 2d games very well, though it can do 2d if needed.

Flash - Market Penetration is about 95%, and a large amount of people are using Flash for their games, it's great for 2d, has recently added support for 3d, and has toolsets and libraries out there to make development quick and easy (Flashpunk and Flixel). That said, networking could be a problem (I don't know how performance is on real time networking...), and it only really supports left click (right click is massively useful for an RTS) Flash is becoming more useful for games, but most of these games are single player with high score tables, or similar sorts of things. Some mobile devices (such as Apple's, or low-end Androids) doesn't support Flash, as well.

Javascript/HTML5 - The biggest issue here is that support for HTML5 is not yet 100%. You're cutting out anyone who uses older browsers (such as IE<9). Performance is also a fairly major bottleneck, since Javascript is a bit slower than Flash or Unity plugins. Additionally, even though Javascript can be pretty easy to learn, there are a few minor/major problems with it that can cause new programmers confusion. The trick here is to find a tool or library that can help development. You can probably find some info here: http://html5games.com/

Side note: there's other options out there, but most of them have even less support or market penetration than anything listed here.