Jews have a complex history in Europe. Firm protections given to Jews -- in reality religious minorities -- by Arbroath could have been just as easily abrogated by successors both at Holyrood and at the Quirinal. For example, Calixtus II's "Sicut Judaeis" offered protections to the Jews and, while controversial, the Bull was reaffirmed by several generations of Popes through the 15th century. "Etsi Judaeorum" was issued by Gregory IX to further drive the point of religious tolerance home but, hardly 15 years later, Innocent IV issued "Impia gens" ordering the burning of select Jewish religious documents. Like all minority ethnic groups, the fate of the Jewish community in any given state was dependent on a wide variety of factors.

As to why the Jewish community failed to settle in Scotland -- this could be anyone's guess. Building upon /u/Redtschorn's earlier comments, a lack of serious economic activity in Edinburgh could have hindered Jewish settlement. Going to a new land with no history of a Jewish community could have deterred settlers and, for all we know, there could have been an implicit understanding that Holyrood was not amenable to Jews despite a lack of written legal documentation.

This will be probably be too simplistic an answer for AskHistorians, but probably because Scotland was too poor.

This is an interesting article from the Jewish Virtual Library.

"Unlike the Jews of England, the Jews of Scotland have enjoyed an uninterrupted history since there seem to have been no Jews in Scotland prior to 1290, when the Jews were expelled from England. Individual Jews did, however, have interests in Scotland without actually settling there, as shown by an official regulation passed in 1180 by the Bishop of Glasgow forbidding churchmen to, "ledge their benefices for money borrowed from Jews.""

If they were restricted to such activities as commerce and money lending, there might not have been enough incentive to remain in a relatively poor, largely agricultural country like Scotland.