It is inferred that the Jedi were able to secretly land on the planet, and that the outlying Confederate forces that would have detected the Republic fleet were destroyed before they could warn the rest of the planet of their approach.
If we are willing to accept the legitimacy of EU sources, it is detailed in the Clone Wars game (released years ago, no relation to the current TV series) how advance Jedi forces landed clandestinely ahead of the Republic fleet (since Yoda left for Kamino and Windu's Jedi for Geonosis simultaneously) and destroyed a few small outposts and such on the way to the arena.
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"For of all sad words of tongue or pen, The saddest are these: 'It might have been!'" -John Whittier
"Apathy is death." -Kreia