The condemning media attention from a respected party like the EFF may harm their reputation. It also ties up legal resources — they probably target people that

The condemning media attention from a respected party like the EFF may harm their reputation. It also ties up legal resources — they probably target people that they expect will fold to their demands due to the high cost of resisting them. Also, if the EFF is successful, the US patent office might use this as an example of frivolous patents that should never have been granted in the first place to resist the legislation mentioned that would make it harder to prevent such bogus patents in the first place.