value for the model that assign to the checkbox is boolean whether it is true or false, unless you define the value. but again it is only 2 options value.
so, rather than using id as model attribute, you might change it to some attribute that could store boolean value. why not using 'isSelected'
<div ng-controller="quoteController" ng-app="MyApp" class="benefits-container">
<!-- benefits -->
<div class="benefit" ng-class="{'selected': pe.id}" ng-repeat="pe in policyEnhancementsArr | filter: {type:'optional'}">
<div class="top">
<md-checkbox ng-model="pe.isSelected" class="blue"></md-checkbox>
<h5 class="item">{{pe.name}}</h5>
<h5 class="prize">{{pe.loading}}</h5>
</div>
<div class="bottom">
<p>{{pe.limitDisplay}}</p>
</div>
</div>
</div>
then update some isSelected value:
...
{
"id": "PVC022",
"name": "NCD Protector",
"limit": null,
"limitDisplay": "N/A",
"desc": "<TBC>",
"type": "optional",
"loading": 0.0,
"isSelected": true
},
...