Meaning of the word 'en'
The en here doesn't mean anything except as part of 'en route', which is imported from French and means 'on or along the way'. See http://www.merriam-webster.com/dictionary/enroute. There are other phrases of this kind, such as 'en banc' or 'en prise'.
There is another word 'en' which is printer's jargon and means the width on the page occupied by the letter 'n' (and is half an 'em').
The word 'en' is actually of French origin. It can mean 'on', 'in', 'inside' or 'along' depending on context. The disambiguation page on Wikipedia says : "En route is a French phrase which means "on the way" or "along the way". "
En is a French preposition that commonly appears in phrases borrowed from French. In this case, en route is a French phrase that means, roughly, on the way (OED).
Other common French loan phrases involving en include:
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en avant - forward. 1823 Ld. Byron Let.
22 Apr. (1980) X. 156 But never mind—‘En Avant!’ live while you can.
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en banc - all or a quorum of judges.
1986 J. Batten Judges 220 Before the Second World War, the appeal courts would sit en banc for the most part.
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en déshabillé - in undress.
1877 C. Reade Woman-hater I. vii. 172 Let me catch her en déshabille, with her porter on one side, and her lover on the other.
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en l'air - in the air, figuratively meaning unsupported.
1964 W. B. Pemberton Battles of Boer War vi. 164 The extreme right of the Boers was practically en l'air and deserted.
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en plein - in full; betting entirely on one side or number in roulette.
1966 C. Robertson Judas Spies i. 9 He had been sitting at a roulette table..playing the even chances mostly, occasionally trying his luck en plein.
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en pointe - dancing on the toe in ballet.
1959 Times 1 Sept. 11/3 Miss Doris Lainë..did a wonderfully neat hop en pointe.
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en poste - in an official (usually diplomatic) position.
1962 John o' London's 31 May 517/1 While he was en poste in Paris he gathered much of the material.
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en suite - forming a suite, often of adjoining rooms.
2006 Peak District Life Spring 33/3 Crisp blue and white striped bed linen and curtains give a fresh feel to the guest bedroom and en-suite bathroom.
Outside of French borrowing, this preposition en is not a generative English word. For instance, en the countertop, en road, or en top of the world don't work, except as an awkward substitution for in or on.