You're probably going to get hassled less about a multitool than a standard knife. After all it's marketed as a tool. However, some rabid idiots might actually check it. Any place that has a 2.5" blade limit, like Boston or a Federal government building might give you a problem. The only common tool that I know of that is under that limit is the Gerber Compact Sport. The SOG Powerlock is close and so are the Leatherman Juice series. One advantage of the SOG tools is that you can always just remove the knife blade. The only multitool that I know of with a knife greater than 3" is the new Leatherman Supertool 200. So if you go into an area with a 3" limit you are technically violating the law. (3" limits are pretty common but it sometimes just covers concealed knives. Wearing it on your belt might solve that problem.) Again a mulitool is less likely than a knife to get you in trouble IMHO.
Unfortunately, airports and buses are another matter........