Most Muslims are not not terrorists. However, some are.
Muslims men are, generally speaking, clearly identifiable due to their appearance. If the good Muslims take offence at the fact that they're being tarred with the same brush as terrorists then maybe they should be more proactive in “outing” the extremists in their religion. However, this almost never happens. More often than not, Muslims with extreme views are concealed and protected from the authorities by their fellow Muslims.
Anyone remember the channel 4 programme, “Undercover Mosque”? This programme showed exactly this type of behaviour. When the “extremists” were in the company of non-Muslims, they kept their views to themselves. The second they thought they were out of earshot, the hate speak started and no one tackled them about it. It was just accepted.
When the IRA was the main terrorist threat in the UK in the 1970s and 1980s, men with Irish accents were routinely singled out, stopped and questioned by police. This is what will happen when any socially identifiable group has a reputation for terrorism.
Right now, it's mainly Muslim men.
Tough.