I think that's a general trend in games and movies: all the good guy's guards and soldiers are easily killed by the enemy, but one person manages to defeat entire armies. I guess Mario is just another series following this trend.
I think that some of Bowser's plans are way too over-the-top for any Toad guard to prevent, such as uprooting the very ground Peach's castle rests on (PM and SMG), using magic to tranform everyone (SMB where Bowser turns everyone into blocks, or SM64 where Bowser traps everyone inside the Castle walls) or clevery takes her when she's not at the castle (SMW, SMS and NSMB). Very few of Bowser's plans involved actually storming the castle.
Also, if the Toads prevented Bowser's kidnappings, then we would have fewer Mario games, wouldn't we ;)?