Here, with a small change in the cheeseonly function you can have an alert before it disables the rest of them, if any of them was checked :
function cheeseonly(onoff){
if(onoff==true &&(document.getElementById('pepperoni').checked==onoff || document.getElementById('olives').checked==onoff || document.getElementById('sausage').checked==onoff || document.getElementById('peppers').checked==onoff || document.getElementById('onions').checked==onoff)){
alert('Other toppings will be disabled.');
}
document.getElementById('pepperoni').disabled=onoff;
document.getElementById('olives').disabled=onoff;
document.getElementById('sausage').disabled=onoff;
document.getElementById('peppers').disabled=onoff;
document.getElementById('onions').disabled=onoff;
if(onoff==true){
document.getElementById('pepperoni').checked=false;
document.getElementById('olives').checked=false;
document.getElementById('sausage').checked=false;
document.getElementById('peppers').checked=false;
document.getElementById('onions').checked=false;
}
}
The code above will simply alert them.
The code here uses confirm which will give them the choice to cancel their action :
function cheeseonly(onoff){
var reply=true;
if(onoff==true &&(document.getElementById('pepperoni').checked==onoff || document.getElementById('olives').checked==onoff || document.getElementById('sausage').checked==onoff || document.getElementById('peppers').checked==onoff || document.getElementById('onions').checked==onoff)){
reply=confirm("Other toppings will be disabled.");
}
if(reply==true){
document.getElementById('pepperoni').disabled=onoff;
document.getElementById('olives').disabled=onoff;
document.getElementById('sausage').disabled=onoff;
document.getElementById('peppers').disabled=onoff;
document.getElementById('onions').disabled=onoff;
if(onoff==true){
document.getElementById('pepperoni').checked=false;
document.getElementById('olives').checked=false;
document.getElementById('sausage').checked=false;
document.getElementById('peppers').checked=false;
document.getElementById('onions').checked=false;
}
}else{
document.getElementById('cheese').checked=false;
}
}