People who are ideologically opposed aside, the biggest problems with jobs that require clearance AFAIK is the cost and turnaround time, meaning that companies may only want to hire people who are already cleared- or you can be sitting around without work for a long time. Many jobs that require clearance also may require work locations that lack the flexibility of other jobs (if you're working on-site for example, then you may have strict working hours, severely locked down workstations with restricted internet access, etc.)
