Bootstrapping is an iterative process. Even if you use a method that doesn't require you to write a loop, the functions you're using will very likely use loops.
Loops likely aren't the bottleneck in your code. Something else it. You could use Matlab's profiler to time your code and produce a summary of time consumption.
Also note Matlab's bootstrapping functions
but depending on what you're bootstrapping, it may be easier to built it yourself.
