What about the market share? If Linux has twice as many online servers as Windows, then it would make sense to have twice as many successful attacks if it has the same amount of security. There is also a huge difference in attacks as has been mentioned. Some attacks aren't a big deal such as web site defacing, but root access however is totally different. One other issue is Linux servers might be more in the spotlight. For instance, if a majority of mainstream sites run on Linux they are more likely to be targeted than some obscure site that doesn't run linux.
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What about the market share? If Linux has twice as many online servers as Windows, then it would make sense to have twice as many successful attacks if it has the same amount of security. There is also a huge difference in attacks as has been mentioned. Some attacks aren't a big deal such as web site defacing, but root access however is totally different. One other issue is Linux servers might be more in the spotlight. For instance, if a majority of mainstream sites run on Linux they are more likely to be targeted than some obscure site that doesn't run linux.