Most likely because it was signed by Sir Robert Howard of Ashtead, Surrey, son of Thomas Howard the 1st Earl of Berkshire. As a royalist, he was made Clerk of Patents in Chancery in June 1660, presumably as a reward. He appears to have stayed in that position until 1664.
Letters patents, including royal charters, are not signed by the Lord Privy Seal. Instead, he formulates the draft into a Writ of Privy Seal and transmits it to the Lord Keeper. The actual document is then drawn up by the Clerk of Patents, who attests to the result with his own signature.
Connecticut received its royal charter in 1662, and Rhode Island in 1663. Both grants were apparently made during Robert Howard's tenure, which explains why they would be signed "Howard".
1. Sir Howard went on to become Member of Parliament for Stockbridge and later Castle Rising, and held the post of Auditor of the Receipts of the Exchequer until his death.
2. Green, Mary Anne Everett, and Francis Lawrance Bickley. Calendar of State Papers, Domestic Series, of the Reign of Charles II: 1660-1685. Vol. 1. HM Stationery Office, 1860.
3. The History of Parliament
4. Bates, Albert Carlos. The Charter of Connecticut: a Study. Connecticut Historical Society, 1932. - "... The actual engrossing of the Patent is done by an officer known as the Clerk of Patents, who at the end indicates the authority under which the Chancery has ordered the Patent to be drawn out, and attests it with his signature. The most common formula is "By writ of Privy Seal" or its Latin equivalent ..."